Highly conserved genes and their use to generate probes and primers for detection of microorganisms

ABSTRACT

Compositions and methods for the detection of vancomycin-resistant pathogens using primers and/or probes to the vanA and vanB genes.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation-in-part of application Ser. No. 11/236,785, filed Sep. 27, 2005, which is a continuation of Ser. No. 10/089,177, filed Mar. 27, 2002, which is the U.S. national phase under 35 U.S.C. §371 of prior PCT International Application No. PCT/CA00/01150, filed Sep. 28, 2000, which claims the benefit of Canada Application No. 2037010 filed May 19, 2000, and Canada Application No. 2283458, filed Sep. 28, 1999, the disclosures of which are hereby expressly incorporated by reference in their entireties. This application is also a continuation-in-part of application Ser. No. 10/753,169, filed Jan. 7, 2004, which is a continuation of application Ser. No. 09/989,643, filed Nov. 20, 2001 which is a continuation of application Ser. No. 09/297,539 filed May 3, 1999 which is a national phase of PCT/CA97/00829 filed Nov. 4, 1997, which claims priority to application Ser. No. 08/743,637, filed Nov. 4, 1996, the disclosures of which are hereby expressly incorporated by reference in their entireties.

SEQUENCE LISTING

The present application is being filed along with duplicate copies of a CD-ROM marked “Copy 1” and “Copy 2” containing a Sequence Listing in electronic format. The duplicate copies of the CD-ROM each contain a file entitled GENOM.048NPCCP1.TXT created on Sep. 14, 2006 and is 1,929,380 bytes in size. The information on these duplicate CD-ROMs is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION Classical Methods for the Identification of Microorganisms

Microorganisms are classically identified by their ability to utilize different substrates as a source of carbon and nitrogen through the use of biochemical tests such as the API20E™ system (bioMérieux). For susceptibility testing, clinical microbiology laboratories use methods including disk diffusion, agar dilution and broth microdilution. Although identifications based on biochemical tests and antibacterial susceptibility tests are cost-effective, generally two days are required to obtain preliminary results due to the necessity of two successive overnight incubations to identify the bacteria from clinical specimens as well as to determine their susceptibility to antimicrobial agents. There are some commercially available automated systems (i.e. the MicroScan™ system from Dade Behring and the Vitek™ system from bioMérieux) which use sophisticated and expensive apparatus for faster microbial identification and susceptibility testing (Stager and Davis, 1992, Clin. Microbiol. Rev. 5:302-327). These systems require shorter incubation periods, thereby allowing most bacterial identifications and susceptibility testing to be performed in less than 6 hours. Nevertheless, these faster systems always require the primary isolation of the bacteria or fungi as a pure culture, a process which takes at least 18 hours for a pure culture or 2 days for a mixed culture. So, the shortest time from sample reception to identification of the pathogen is around 24 hours. Moreover, fungi other than yeasts are often difficult or very slow to grow from clinical specimens. Identification must rely on labor-intensive techniques such as direct microscopic examination of the specimens and by direct and/or indirect immunological assays. Cultivation of most parasites is impractical in the clinical laboratory. Hence, microscopic examination of the specimen, a few immunological tests and clinical symptoms are often the only methods used for an identification that frequently remains presumptive.

The fastest bacterial identification system, the autoSCAN-Walk-Away™ system (Dade Behring) identifies both gram-negative and gram-positive bacterial species from standardized inoculum in as little as 2 hours and gives susceptibility patterns to most antibiotics in 5 to 6 hours. However, this system has a particularly high percentage (i.e. 3.3 to 40.5%) of non-conclusive identifications with bacterial species other than Enterobacteriaceae (Croizé J., 1995, Lett. Infectiol. 10:109-113; York et al., 1992, J. Clin. Microbiol. 30:2903-2910). For Enterobacteriaceae, the percentage of non-conclusive identifications was 2.7 to 11.4%. The list of microorganisms identified by commercial systems based on classical identification methods is given in Table 15.

A wide variety of bacteria and fungi are routinely isolated and identified from clinical specimens in microbiology laboratories. Tables 1 and 2 give the incidence for the most commonly isolated bacterial and fungal pathogens from various types of clinical specimens. These pathogens are the main organisms associated with nosocomial and community-acquired human infections and are therefore considered the most clinically important.

Clinical Specimens Tested in Clinical Microbiology Laboratories

Most clinical specimens received in clinical microbiology laboratories are urine and blood samples. At the microbiology laboratory of the Centre Hospitalier de l'Université Laval (CHUL), urine and blood account for approximately 55% and 30% of the specimens received, respectively (Table 3). The remaining 15% of clinical specimens comprise various biological fluids including sputum, pus, cerebrospinal fluid, synovial fluid, and others (Table 3). Infections of the urinary tract, the respiratory tract and the bloodstream are usually of bacterial etiology and require antimicrobial therapy. In fact, all clinical samples received in the clinical microbiology laboratory are tested routinely for the identification of bacteria and antibiotic susceptibility.

Conventional Pathogen Identification from Clinical Specimens

Urine Specimens

The search for pathogens in urine specimens is so preponderant in the routine microbiology laboratory that a myriad of tests have been developed. However, the gold standard remains the classical semi-quantitative plate culture method in which 1 μL of urine is streaked on agar plates and incubated for 18-24 hours. Colonies are then counted to determine the total number of colony forming units (CFU) per liter of urine. A bacterial urinary tract infection (UTI) is normally associated with a bacterial count of 10⁷ CFU/L or more in urine. However, infections with less than 10⁷ CFU/L in urine are possible, particularly in patients with a high incidence of diseases or those catheterized (Stark and Maki, 1984, N. Engl. J. Med. 311:560-564). Importantly, approximately 80% of urine specimens tested in clinical microbiology laboratories are considered negative (i.e. bacterial count of less than 10⁷ CFU/L; Table 3). Urine specimens found positive by culture are further characterized using standard biochemical tests to identify the bacterial pathogen and are also tested for susceptibility to antibiotics. The biochemical and susceptibility testing normally require 18-24 hours of incubation.

Accurate and rapid urine screening methods for bacterial pathogens would allow a faster identification of negative specimens and a more efficient treatment and care management of patients. Several rapid identification methods (Uriscreen™, UTIscreen™, Flash Track™ DNA probes and others) have been compared to slower standard biochemical methods, which are based on culture of the bacterial pathogens. Although much faster, these rapid tests showed low sensitivities and poor specificities as well as a high number of false negative and false positive results (Koening et al., 1992, J. Clin. Microbiol. 30:342-345; Pezzlo et al., 1992, J. Clin. Microbiol. 30:640-684).

Blood Specimens

The Blood Specimens Received In The Microbiology Laboratory Are Always Submitted For Culture. Blood Culture Systems May Be Manual, Semi-Automated Or Completely Automated. The BACTEC™ System (From Becton Dickinson) And The Bactalert™ System (From Organon Teknika Corporation) Are The Two Most Widely Used Automated Blood Culture Systems. These Systems Incubate Blood Culture Bottles Under Optimal Conditions For Growth Of Most Bacteria. Bacterial Growth Is Monitored Continuously To Detect Early Positives By Using Highly Sensitive Bacterial Growth Detectors. Once Growth Is Detected, A Gram Stain Is Performed Directly From The Blood Culture And Then Used To Inoculate Nutrient Agar Plates. Subsequently, Bacterial Identification And Susceptibility Testing Are Carried Out From Isolated Bacterial Colonies With Automated Systems As Described Previously. Blood Culture Bottles Are Normally Reported As Negative If No Growth Is Detected After An Incubation Of 6 To 7 Days. Normally, The Vast Majority Of Blood Cultures Are Reported Negative. For Example, The Percentage Of Negative Blood Cultures At The Microbiology Laboratory Of The CHUL For The Period February 1994-January 1995 Was 93.1% (Table 3).

Other Clinical Samples

Upon receipt by the clinical microbiology laboratory, all body fluids other than blood and urine that are from normally sterile sites (i.e. cerebrospinal, synovial, pleural, pericardial and others) are processed for direct microscopic examination and subsequent culture. Again, most clinical samples are negative for culture (Table 3). In all these normally sterile sites, tests for the universal detection of algae, archaea, bacteria, fungi and parasites would be very useful.

Regarding clinical specimens which are not from sterile sites such as sputum or stool specimens, the laboratory diagnosis by culture is more problematic because of the contamination by the normal flora. The bacterial or fungal pathogens potentially associated with the infection are grown and separated from the colonizing microbes using selective methods and then identified as described previously. Of course, the DNA-based universal detection of bacteria would not be useful for the diagnosis of bacterial infections at these non-sterile sites. On the other hand, DNA-based assays for species or genus or family or group detection and identification as well as for the detection of antimicrobial agents resistance genes from these specimens would be very useful and would offer several advantages over classical identification and susceptibility testing methods.

DNA-Based Assays with any Specimen

There is an obvious need for rapid and accurate diagnostic tests for the detection and identification of algae, archaea, bacteria, fungi and parasites directly from clinical specimens. DNA-based technologies are rapid and accurate and offer a great potential to improve the diagnosis of infectious diseases (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.; Bergeron and Ouellette, 1995, Infection 23:69-72; Bergeron and Ouellette, 1998, J Clin Microbiol. 36:2169-72). The DNA probes and amplification primers which are objects of the present invention are applicable for the detection and identification of algae, archaea, bacteria, fungi, and parasites directly from any clinical specimen such as blood, urine, sputum, cerebrospinal fluid, pus, genital and gastro-intestinal tracts, skin or any other type of specimens (Table 3). These assays are also applicable to detection from microbial cultures (e.g. blood cultures, bacterial or fungal colonies on nutrient agar, or liquid cell cultures in nutrient broth). The DNA-based tests proposed in this invention are superior in terms of both rapidity and accuracy to standard biochemical methods currently used for routine diagnosis from any clinical specimens in microbiology laboratories. Since these tests can be performed in one hour or less, they provide the clinician with new diagnostic tools which should contribute to a better management of patients with infectious diseases. Specimens from sources other than humans (e.g. other primates, birds, plants, mammals, farm animals, livestock, food products, environment such as water or soil, and others) may also be tested with these assays.

A High Percentage of Culture-Negative Specimens

Among all the clinical specimens received for routine diagnosis, approximately 80% of urine specimens and even more (around 95%) for other types of normally sterile clinical specimens are negative for the presence of bacterial pathogens (Table 3). It would also be desirable, in addition to identify bacteria at the species or genus or family or group level in a given specimen, to screen out the high proportion of negative clinical specimens with a DNA-based test detecting the presence of any bacterium (i.e. universal bacterial detection). As disclosed in the present invention, such a screening test may be based on DNA amplification by PCR of a highly conserved genetic target found in all bacteria. Specimens negative for bacteria would not be amplified by this assay. On the other hand, those that are positive for any bacterium would give a positive amplification signal. Similarly, highly conserved genes of fungi and parasites could serve not only to identify particular species or genus or family or group but also to detect the presence of any fungi or parasite in the specimen.

Towards the Development of Rapid DNA-Based Diagnostic Tests

A rapid diagnostic test should have a significant impact on the management of infections. DNA probe and DNA amplification technologies offer several advantages over conventional methods for the identification of pathogens and antimicrobial agents resistance genes from clinical samples (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.; Ehrlich and Greenberg, 1994, PCR-based Diagnostics in Infectious Disease, Blackwell Scientific Publications, Boston, Mass.). There is no need for culture of the pathogens, hence the organisms can be detected directly from clinical samples, thereby reducing the time associated with the isolation and identification of pathogens. Furthermore, DNA-based assays are more accurate for microbial identification than currently used phenotypic identification systems which are based on biochemical tests and/or microscopic examination. Commercially available DNA-based technologies are currently used in clinical microbiology laboratories, mainly for the detection and identification of fastidious bacterial pathogens such as Mycobacterium tuberculosis, Chlamydia trachomatis, Neisseria gonorrhoeae as well as for the detection of a variety of viruses (Tang Y. and Persing D. H., Molecular detection and identification of microorganisms, In: P. Murray et al., 1999, Manual of Clinical Microbiology, ASM press, 7^(th) edition, Washington D.C.). There are also other commercially available DNA-based assays which are used for culture confirmation assays.

Others have developed DNA-based tests for the detection and identification of bacterial pathogens which are objects of the present invention, for example: Staphylococcus sp. (U.S. Pat. No. 5,437,978), Neisseria sp. (U.S. Pat. No. 5,162,199 and European patent serial no. 0,337,896,131) and Listeria monocytogenes (U.S. Pat. Nos. 5,389,513 and 5,089,386). However, the diagnostic tests described in these patents are based either on rRNA genes or on genetic targets different from those described in the present invention. To our knowledge there are only four patents published by others mentioning the use of any of the four highly conserved gene targets described in the present invention for diagnostic purposes (PCT international publication number WO92/03455 and WO00/14274, European patent publication number 0 133 671 B1, and European patent publication number 0 133 288 A2). WO92/03455 is focused on the inhibition of Candida species for therapeutic purposes. It describes antisense oligonucleotide probes hybridizing to Candida messenger RNA. Two of the numerous mRNA proposed as targets are coding for translation elongation factor 1 (tef1) and the beta subunit of ATPase. DNA amplification or hybridization are not under the scope of their invention and although diagnostic use is briefly mentioned in the body of the application, no specific claim is made regarding diagnostics. WO00/14274 describes the use of bacterial recA gene for identification and speciation of bacteria of the Burkholderia cepacia complex. Specific claims are made on a method for obtaining nucleotide sequence information for the recA gene from the target bacteria and a following comparison with a standard library of nucleotide sequence information (claim 1), and on the use of PCR for amplification of the recA gene in a sample of interest (claims 4 to 7, and 13). However, the use of a discriminatory restriction enzyme in a RFLP procedure is essential to fulfill the speciation and WO00/14274 did not mention that multiple recA probes could be used simultaneously. Patent EP 0 133 288 A2 describes and claims the use of bacterial tuf (and fus) sequence for diagnostics based on hybridization of a tuf (or fus) probe with bacterial DNA. DNA amplification is not under the scope of EP 0 133 288 A2. Nowhere it is mentioned that multiple tuf (or fus) probes could be used simultaneously. No mention is made regarding speciation using tuf (or fus) DNA nucleic acids and/or sequences. The sensitivities of the tuf hybridizations reported are 1×10⁶ bacteria or 1-100 ng of DNA. This is much less sensitive than what is achieved by our assays using nucleic acid amplification technologies.

Although there are phenotypic identification methods which have been used for more than 125 years in clinical microbiology laboratories, these methods do not provide information fast enough to be useful in the initial management of patients. There is a need to increase the speed of the diagnosis of commonly encountered bacterial, fungal and parasitical infections. Besides being much faster, DNA-based diagnostic tests are more accurate than standard biochemical tests presently used for diagnosis because the microbial genotype (e.g. DNA level) is more stable than the phenotype (e.g. physiologic level).

Bacteria, fungi and parasites encompass numerous well-known microbial pathogens. Other microorganisms could also be pathogens or associated with human diseases. For example, achlorophylious algae of the Prototheca genus can infect humans. Archae, especially methanogens, are present in the gut flora of humans (Reeve, J. H., 1999, J. Bacteriol. 181:3613-3617). However, methanogens have been associated to pathologic manifestations in the colon, vagina, and mouth (Belay et al., 1988, Appl. Enviro. Microbiol. 54:600-603; Belay et al., 1990, J. Clin. Microbiol. 28:1666-1668; Weaver et al., 1986, Gut 27:698-704).

In addition to the identification of the infectious agent, it is often desirable to identify harmful toxins and/or to monitor the sensitivity of the microorganism to antimicrobial agents. As revealed in this invention, genetic identification of the microorganism could be performed simultaneously with toxin and antimicrobial agents resistance genes. Alternatively, assays to identify toxin and/or antimicrobial resistance genes can be performed separately and independently from assays for identification of infectious agents.

Knowledge of the genomic sequences of algal, archaeal, bacterial, fungal and parasitical species continuously increases as testified by the number of sequences available from public databases such as GenBank. From the sequences readily available from those public databases, there is no indication therefrom as to their potential for diagnostic purposes. For determining good candidates for diagnostic purposes, one could select sequences for DNA-based assays for (i) the species-specific detection and identification of commonly encountered bacterial, fungal and parasitical pathogens, (ii) the genus-specific detection and identification of commonly encountered bacterial, fungal or parasitical pathogens, (iii) the family-specific detection and identification of commonly encountered bacterial, fungal or parasitical pathogens; (iv) the group-specific detection and identification of commonly encountered bacterial, fungal or parasitical pathogens, (v) the universal detection of algal, archaeal, bacterial, fungal or parasitical pathogens, and/or (vi) the specific detection and identification of antimicrobial agents resistance genes, and/or (vii) the specific detection and identification of bacterial toxin genes. All of the above types of DNA-based assays may be performed directly from any type of clinical specimens or from a microbial culture.

In our assigned U.S. Pat. No. 6,001,564 and our WO98/20157 patent publication, we described DNA sequences suitable for (i) the species-specific detection and identification of clinically important bacterial pathogens, (ii) the universal detection of bacteria, and (iii) the detection of antimicrobial agents resistance genes.

The WO98/20157 patent publication describes proprietary tuf DNA sequences as well as tuf sequences selected from public databases (in both cases, fragments of at least 100 base pairs), as well as oligonucleotide probes and amplification primers derived from these sequences. All the nucleic acid sequences described in that patent publication can enter in the composition of diagnostic kits or products and methods capable of a) detecting the presence of bacteria and fungi b) detecting specifically at the species, genus, family or group levels, the presence of bacteria and fungi and antimicrobial agents resistance genes associated with these pathogens. However, these methods and kits need to be improved, since the ideal kit and method should be capable of diagnosing close to 100% of microbial pathogens and associated antimicrobial agents resistance genes and toxins genes. For example, infections caused by Enterococcus faecium have become a clinical problem because of its resistance to many antibiotics. Both the detection of these bacteria and the evaluation of their resistance profiles are desirable. Besides that, novel DNA sequences (probes and primers) capable of recognizing the same and other microbial pathogens or the same and additional antimicrobial agents resistance genes are also desirable to aim at detecting more target genes and complement our earlier patent applications.

The present invention improves the assigned application by disclosing new proprietary tuf nucleic acids and/or sequences as well as describing new ways to obtain tuf nucleic acids and/or sequences. In addition we disclose new proprietary atpD and recA nucleic acids and/or sequences. In addition, new uses of tuf, atpD and recA DNA nucleic acids and/or sequences selected from public databases (Table 11) are disclosed.

Highly Conserved Genes for Identification and Diagnostics

Highly conserved genes are useful for identification of microorganisms. For bacteria, the most studied genes for identification of microorganisms are the universally conserved ribosomal RNA genes (rRNA). Among those, the principal targets used for identification purposes are the small subunit (SSU) ribosomal 16S rRNA genes (in prokaryotes) and 18S rRNA genes (in eukaryotes) (Relman and Persing, Genotyping Methods for Microbial Identification, In: D. H. Persing, 1996, PCR Protocols for Emerging Infectious Diseases, ASM Press, Washington D.C.). The rRNA genes are also the most commonly used targets for universal detection of bacteria (Chen et al., 1988, FEMS Microbiol. Lett. 57:19-24; McCabe et al., 1999, Mol. Genet. Metabol. 66:205-211) and fungi (Van Burik et al., 1998, J. Clin. Microbiol. 36:1169-1175).

However, it may be difficult to discriminate between closely related species when using primers derived from the 16S rRNA. In some instances, 16S rRNA sequence identity may not be sufficient to guarantee species identity (Fox et al., 1992, Int. J. Syst. Bacteriol. 42:166-170) and it has been shown that inter-operon sequence variation as well as strain to strain variation could undermine the application of 16S rRNA for identification purposes (Clayton et al., 1995, Int. J. Syst. Bacteriol. 45:595-599). The heat shock proteins (HSP) are another family of very conserved proteins. These ubiquitous proteins in bacteria and eukaryotes are expressed in answer to external stress agents. One of the most described of these HSP is HSP 60. This protein is very conserved at the amino acid level, hence it has been useful for phylogenetic studies. Similar to 16S rRNA, it would be difficult to discriminate between species using the HSP 60 nucleotide sequences as a diagnostic tool. However, Goh et al. identified a highly conserved region flanking a variable region in HSP 60, which led to the design of universal primers amplifying this variable region (Goh et al., U.S. Pat. No. 5,708,160). The sequence variations in the resulting amplicons were found useful for the design of species-specific assays.

SUMMARY OF THE INVENTION

Disclosed herein are compositions and methods for the detection and quantitation of antibiotic resistant organisms from a sample.

Some embodiments relate to compositions for the detection of a vancomycin resistant pathogen in a sample using a nucleic acid amplification assay. The composition can include at least one primer pair, comprising a forward and a reverse oligonucleotide, wherein the forward and reverse oligonucleotides each includes a binding region that is complementary to primer binding sites present on opposite strands of the pathogen's DNA, wherein the primer pair is adapted to amplify a vanA or vanB gene of the pathogen's DNA between and including said primer binding sites to produce a detectable amplification product. The binding regions of the oligonucleotides can correspond to, or be fully complementary to, at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 consecutive nucleotides of at least two of the following sequences: SEQ ID NO: 1090, SEQ ID NO: 1091, SEQ ID NO: 1095, SEQ ID NO: 2298 and SEQ ID NO: 1096.

In some embodiments, the composition includes a primer pair wherein the primers comprise, consist essentially of, or consist of at least 10 consecutive nucleotides of SEQ ID NO: 1095 and SEQ ID NO: 1096. Preferred compositions include a primer pair wherein the primers comprises, consists essentially of, or consist of the sequences of SEQ ID NO: 1095 and SEQ ID NO: 1096.

Preferably, the composition comprises at least four primers, wherein the each of the four primers comprises, consists essentially of, or consists of at least 10 consecutive nucleotides of SEQ ID NOs: 1090, 1091, 1096 and 2298, or the complements thereof. In other preferred embodiments, the four primers comprise, consist essentially of, or consist of the SEQ ID NO: 1090, 1091, 1096, and 2298.

In some embodiments, the composition can also include at least one internal hybridization probe, wherein the internal hybridization probe can hybridize under stringent condition to the vanA or vanB amplification products produced by the compositions described above. Preferably, the internal hybridization probe is a molecular beacon. In more preferred embodiments, the molecular beacon can include the sequence of SEQ ID NO: 2299 or SEQ ID NO: 2300.

In further embodiments, the compositions can also include at least one internal control DNA, which can be amplified to produce an internal control amplicon under the same conditions and using the same oligonucleotides of the compositions described above. In further embodiments, the compositions can include an internal control probe that can hybridize under stringent conditions to the internal control amplicon. In some embodiments, the internal control DNA comprises the sequence of SEQ ID NO: 2302. Preferably, the internal control probe is a molecular beacon. In some embodiments, the internal control probe includes at least 10 consecutive nucleotides of the sequence of SEQ ID NO: 2301.

Also provided herein are kits that include the compositions described herein.

Methods to detect the presence of vancomycin-resistant organisms in a sample are also provided. In some embodiments, the method can include the step of annealing the nucleic acids of the sample with at least one probe and/or primer, wherein each of the primers and/or probes include nucleic acid sequences that correspond to, or are fully complementary to, at least 10 consecutive nucleotides of at least two of the following sequences: SEQ ID NO: 1090, SEQ ID NO: 1091, SEQ ID NO: 1095 and SEQ ID NO: 1096. The presence and/or amount of primer or probe that is annealed to said sample nucleic acid can be detected. In some embodiments, the primers and/or probes can include the nucleic acid sequences of SEQ ID NO's 1090, 1091, 1096 and 2297, or the complements thereof.

Preferably, the primers and/or probes are placed in the same physical enclosure.

In some embodiments, wherein at least one pair of primers is annealed to the sample DNA, and wherein said primer pair include nucleic acid sequences that correspond to, or are fully complementary to, at least 10 consecutive nucleotides of SEQ ID NO: 1090 and 1091 or SEQ ID NO: 1095 and 1096, the methods also include a step of amplifying the sample DNA with the annealed primer pair(s). For example, in some embodiments, the amplification step can include a method selected from the group consisting of:

(a) polymerase chain reaction (PCR),

(b) ligase chain reaction,

(c) nucleic acid sequence-based amplification,

(d) self-sustained sequence replication,

(e) strand displacement amplification,

(f) branched DNA signal amplification,

(g) nested PCR, and

(h) multiplex PCR.

Preferably, the amplification step includes a PCR amplification step.

In some embodiments that include an amplification step, the sample can also be contacted with at least one probe that hybridizes to an amplification product produced from at least one of the primer pairs. In preferred embodiments, the probe includes at least 10 consecutive nucleotides of the sequence of SEQ ID NO: 2299 or 2300. For example, in some embodiments, the at least one probe includes the sequence of SEQ ID NO: 2299 or 2300.

It is an object of the present invention to provide a specific, ubiquitous and sensitive method using probes and/or amplification primers for determining the presence and/or amount of nucleic acids:

-   -   from any algal, archaeal, bacterial, fungal or parasitical         species in any sample suspected of containing said nucleic         acids, and optionally,     -   from specific microbial species or genera selected from the         group consisting of the species or genera listed in Table 4, and         optionally,     -   from an antimicrobial agents resistance gene selected from the         group consisting of the genes listed in Table 5, and optionally,     -   from a toxin gene selected from the group consisting of the         genes listed in Table 6,         -   wherein each of said nucleic acids or a variant or part             thereof comprises a selected target region hybridizable with             said probes or primers;         -   said method comprising the steps of contacting said sample             with said probes or primers and detecting the presence             and/or amount of hybridized probes or amplified products as             an indication of the presence and/or amount of said any             microbial species, specific microbial species or genus or             family or group and antimicrobial agents resistance gene             and/or toxin gene.

In a specific embodiment, a similar method directed to each specific microbial species or genus or family or group detection and identification, antimicrobial agents resistance genes detection, toxin genes detection, and universal bacterial detection, separately, is provided.

In a more specific embodiment, the method makes use of DNA fragments from conserved genes (proprietary sequences and sequences obtained from public databases), selected for their capacity to sensitively, specifically and ubiquitously detect the targeted algal, archaeal, bacterial, fungal or parasitical nucleic acids.

In a particularly preferred embodiment, oligonucleotides of at least 12 nucleotides in length have been derived from the longer DNA fragments, and are used in the present method as probes or amplification primers. To be a good diagnostic candidate, an oligonucleotide of at least 12 nucleotides should be capable of hybridizing with nucleic acids from given microorganism(s), and with substantially all strains and representatives of said microorganism(s); said oligonucleotide being species-, or genus-, or family-, or group-specific or universal.

In another particularly preferred embodiment, oligonucleotides primers and probes of at least 12 nucleotides in length are designed for their specificity and ubiquity based upon analysis of our databases of tuf, atpD and recA sequences. These databases are generated using both proprietary and public sequence information. Altogether, these databases form a sequence repertory useful for the design of primers and probes for the detection and identification of algal, archaeal, bacterial, fungal and parasitical microorganisms. The repertory can also be subdivided into subrepertories for sequence analysis leading to the design of various primers and probes.

The tuf, atpD and recA sequences databases as a product to assist the design of oligonucleotides primers and probes for the detection and identification of algal, archaeal, bacterial, fungal and parasitical microorganisms are also covered.

The proprietary oligonucleotides (probes and primers) are also another object of this invention.

Diagnostic kits comprising probes or amplification primers such as those for the detection of a microbial species or genus or family or phylum or group selected from the following list consisting of Abiotrophia adiacens, Acinetobacter baumanii, Actinomycetae, Bacteroides, Cytophaga and Flexibacter phylum, Bacteroides fragilis, Bordetella pertussis, Bordetella sp., Campylobacter jejuni and C. coli, Candida albicans, Candida dubliniensis, Candida glabrata, Candida guilliermondii, Candida krusei, Candida lusitaniae, Candida parapsilosis, Candida tropicalis, Candida zeylanoides, Candida sp., Chlamydia pneumoniae, Chlamydia trachomatis, Clostridium sp., Corynebacterium sp., Crypococcus neoformans, Cryptococcus sp., Cryptosporidium parvum, Entamoeba sp., Enterobacteriaceae group, Enterococcus casseliflavus-flavescens-gallinarum group, Enterococcus faecalis, Enterococcus faecium, Enterococcus gallinarum, Enterococcus sp., Escherichia coli and Shigella sp. group, Gemella sp., Giardia sp., Haemophilus influenzae, Klebsiella pneumoniae, Legionella pneumophila, Legionella sp., Leishmania sp., Mycobacteriaceae family, Mycoplasma pneumoniae, Neisseria gonorrhoeae, platelets contaminants group (see Table 14), Pseudomonas aeruginosa, Pseudomonads group, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus saprophyticus, Staphylococcus sp., Streptococcus agalactiae, Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus sp., Trypanosoma brucei, Trypanosoma cruzi, Trypanosoma sp., Trypanosomatidae family, are also objects of the present invention.

Diagnostic kits further comprising probes or amplification primers for the detection of an antimicrobial agents resistance gene selected from the group listed in Table 5 are also objects of this invention.

Diagnostic kits further comprising probes or amplification primers for the detection of a toxin gene selected from the group listed in Table 6 are also objects of this invention.

Diagnostic kits further comprising probes or amplification primers for the detection of any other algal, archaeal, bacterial, fungal or parasitical species than those specifically listed herein, comprising or not comprising those for the detection of the specific microbial species or genus or family or group listed above, and further comprising or not comprising probes and primers for the antimicrobial agents resistance genes listed in Table 5, and further comprising or not comprising probes and primers for the toxin genes listed in Table 6 are also objects of this invention.

In a preferred embodiment, such a kit allows for the separate or the simultaneous detection and identification of the above-listed microbial species or genus or family or group; or universal detection of algae, archaea, bacteria, fungi or parasites; or antimicrobial agents resistance genes; or toxin genes; or for the detection of any microorganism (algae, archaea, bacteria, fungi or parasites).

In the above methods and kits, probes and primers are not limited to nucleic acids and may include, but are not restricted to analogs of nucleotides such as: inosine, 3-nitropyrrole nucleosides (Nichols et al., 1994, Nature 369:492-493), Linked Nucleic Acids (LNA) (Koskin et al., 1998, Tetrahedron 54:3607-3630), and Peptide Nucleic Acids (PNA) (Egholm et al., 1993, Nature 365:566-568).

In the above methods and kits, amplification reactions may include but are not restricted to: a) polymerase chain reaction (PCR), b) ligase chain reaction (LCR), c) nucleic acid sequence-based amplification (NASBA), d) self-sustained sequence replication (3SR), e) strand displacement amplification (SDA), f) branched DNA signal amplification (bDNA), g) transcription-mediated amplification (TMA), h) cycling probe technology (CPT), i) nested PCR, j) multiplex PCR, k) solid phase amplification (SPA), 1) nuclease dependent signal amplification (NDSA), m) rolling circle amplification technology (RCA), n) Anchored strand displacement amplification, o) Solid-phase (immobilized) rolling circle amplification.

In the above methods and kits, detection of the nucleic acids of target genes may include real-time or post-amplification technologies. These detection technologies can include, but are not limited to, fluorescence resonance energy transfer (FRET)-based methods such as adjacent hybridization to FRET probes (including probe-probe and probe-primer methods), TaqMan, Molecular Beacons, scorpions, nanoparticle probes and Sunrise (Amplifluor). Other detection methods include target genes nucleic acids detection via immunological methods, solid phase hybridization methods on filters, chips or any other solid support, whether the hybridization is monitored by fluorescence, chemiluminescence, potentiometry, mass spectrometry, plasmon resonance, polarimetry, colorimetry, or scanometry. Sequencing, including sequencing by dideoxy termination or sequencing by hybridization, e.g. sequencing using a DNA chip, is another possible method to detect and identify the nucleic acids of target genes.

In a preferred embodiment, a PCR protocol is used for nucleic acid amplification, in diagnostic method as well as in method of construction of a repertory of nucleic acids and deduced sequences.

In a particularly preferred embodiment, a PCR protocol is provided, comprising, an initial denaturation step of 1-3 minutes at 95° C., followed by an amplification cycle including a denaturation step of one second at 95° C. and an annealing step of 30 seconds at 45-65° C., without any time allowed specifically for the elongation step. This PCR protocol has been standardized to be suitable for PCR reactions with most selected primer pairs, which greatly facilitates the testing because each clinical sample can be tested with universal, species-specific, genus-specific, antimicrobial agents resistance gene and toxin gene PCR primers under uniform cycling conditions. Furthermore, various combinations of primer pairs may be used in multiplex PCR assays.

It is also an object of the present invention that tuf, atpD and recA sequences could serve as drug targets and these sequences and means to obtain them revealed in the present invention can assist the screening, design and modeling of these drugs.

It is also an object of the present invention that tuf, atpD and recA sequences could serve for vaccine purposes and these sequences and means to obtain them revealed in the present invention can assist the screening, design and modeling of these vaccines.

We aim at developing a universal DNA-based test or kit to screen out rapidly samples which are free of algal, archaeal, bacterial, fungal or parasitical cells. This test could be used alone or combined with more specific identification tests to detect and identify the above algal and/or archaeal and/or bacterial and/or fungal and/or parasitical species and/or genera and/or family and/or group and to determine rapidly the bacterial resistance to antibiotics and/or presence of bacterial toxins. Although the sequences from the selected antimicrobial agents resistance genes are available from public databases and have been used to develop DNA-based tests for their detection, our approach is unique because it represents a major improvement over current diagnostic methods based on bacterial cultures. Using an amplification method for the simultaneous or independent or sequential microbial detection-identification and antimicrobial resistance genes detection, there is no need for culturing the clinical sample prior to testing. Moreover, a modified PCR protocol has been developed to detect all target DNA sequences in approximately one hour under uniform amplification conditions. This procedure should save lives by optimizing treatment, should diminish antimicrobial agents resistance because less antibiotics will be prescribed, should reduce the use of broad spectrum antibiotics which are expensive, decrease overall health care costs by preventing or shortening hospitalizations, and side effects of drugs, and decrease the time and costs associated with clinical laboratory testing.

In another embodiment, sequence repertories and ways to obtain them for other gene targets are also an object of this invention, such is the case for the hexA nucleic acids and/or sequences of Streptococci.

In yet another embodiment, for the detection of mutations associated with antibiotic resistance genes, we built repertories to distinguish between point mutations reflecting only gene diversity and point mutations involved in resistance. Such repertories and ways to obtain them for pbp1a, pbp2b and pbp2x genes of sensitive and penicillin-resistant Streptococcus pneumoniae and also for gyrA and parC gene fragments from various bacterial species are also an object of the present invention.

The diagnostic kits, primers and probes mentioned above can be used to identify algae, archaea, bacteria, fungi, parasites, antimicrobial agents resistance genes and toxin genes on any type of sample, whether said diagnostic kits, primers and probes are used for in vitro or in situ applications. The said samples may include but are not limited to: any clinical sample, any environment sample, any microbial culture, any microbial colony, any tissue, and any cell line.

It is also an object of the present invention that said diagnostic kits, primers and probes can be used alone or in conjunction with any other assay suitable to identify microorganisms, including but not limited to: any immunoassay, any enzymatic assay, any biochemical assay, any lysotypic assay, any serological assay, any differential culture medium, any enrichment culture medium, any selective culture medium, any specific assay medium, any identification culture medium, any enumeration culture medium, any cellular stain, any culture on specific cell lines, and any infectivity assay on animals.

In the methods and kits described herein below, the oligonucleotide probes and amplification primers have been derived from larger sequences (i.e. DNA fragments of at least 100 base pairs). All DNA fragments have been obtained either from proprietary fragments or from public databases. DNA fragments selected from public databases are newly used in a method of detection according to the present invention, since they have been selected for their diagnostic potential.

In another embodiment, the amino acid sequences translated from the repertory of tuf, atpD and recA nucleic acids and/or sequences are also an object of the present invention.

It is clear to the individual skilled in the art that other oligonucleotide sequences appropriate for (i) the universal detection of algae, archaea, bacteria, fungi or parasites, (ii) the detection and identification of the above microbial species or genus or family or group, and (iii) the detection of antimicrobial agents resistance genes, and (iv) the detection of toxin genes, other than those listed in Annexes I to III, XXI to XXII, XXXII to XXXVII, XXXIX to XLI, and XLIII to LIV may also be derived from the proprietary fragments or selected public database sequences. For example, the oligonucleotide primers or probes may be shorter or longer than the ones chosen; they may also be selected anywhere else in the proprietary DNA fragments or in the sequences selected from public databases; they may be also variants of the same oligonucleotide. If the target DNA or a variant thereof hybridizes to a given oligonucleotide, or if the target DNA or a variant thereof can be amplified by a given oligonucleotide PCR primer pair, the converse is also true; a given target DNA may hybridize to a variant oligonucleotide probe or be amplified by a variant oligonucleotide PCR primer. Alternatively, the oligonucleotides may be designed from any DNA fragment sequences for use in amplification methods other than PCR. Consequently, the core of this invention is the identification of universal, species-specific, genus-specific, family-specific, group-specific, resistance gene-specific, toxin gene-specific genomic or non-genomic DNA fragments which are used as a source of specific and ubiquitous oligonucleotide probes and/or amplification primers. Although the selection and evaluation of oligonucleotides suitable for diagnostic purposes requires much effort, it is quite possible for the individual skilled in the art to derive, from the selected DNA fragments, oligonucleotides other than the ones listed in Annexes I to III, XXI to XXII, XXXII to XXXVII, XXXIX to XLI, and XLIII to LIV which are suitable for diagnostic purposes. When a proprietary fragment or a public databases sequence is selected for its specificity and ubiquity, it increases the probability that subsets thereof will also be specific and ubiquitous.

Since a high percentage of clinical specimens are negative for bacteria (Table 3), DNA fragments having a high potential for the selection of universal oligonucleotide probes or primers were selected from proprietary and public database sequences. The amplification primers were selected from genes highly conserved in algae, archaea, bacteria, fungi and parasites, and are used to detect the presence of any algal, archaeal, bacterial, fungal or parasitical pathogen in clinical specimens in order to determine rapidly whether it is positive or negative for algae, archaea, bacteria, fungi or parasites. The selected genes, designated tuf, fus, atpD and recA, encode respectively 2 proteins (elongation factors Tu and G) involved in the translational process during protein synthesis, a protein (beta subunit) responsible for the catalytic activity of proton pump ATPase and a protein responsible for the homologous recombination of genetic material. The alignments of tuf, atpD and recA sequences used to derive the universal primers include both proprietary and public database sequences. The universal primer strategy allows the rapid screening of the numerous negative clinical specimens (around 80% of the specimens received, see Table 3) submitted for microbiological testing.

Table 4 provides a list of the archaeal, bacterial, fungal and parasitical species for which tuf and/or atpD and/or recA nucleic acids and/or sequences are revealed in the present invention. Tables 5 and 6 provide a list of antimicrobial agents resistance genes and toxin genes selected for diagnostic purposes. Table 7 provides the origin of tuf, atpD and recA nucleic acids and/or sequences listed in the sequence listing. Tables 8-10 and 12-14 provide lists of species used to test the specificity, ubiquity and sensitivity of some assays described in the examples. Table 11 provides a list of microbial species for which tuf and/or atpD and/or recA sequences are available in public databases. Table 15 lists the microorganisms identified by commercial systems. Tables 16-18 are part of Example 42, whereas Tables 19-20 are part of Example 43. Tables 21-22 illustrate Example 44, whereas Tables 23-25 illustrate Example 45.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1 and 2 illustrate the principal subdivisions of the tuf and atpD sequences repertories, respectively. For the design of primers and probes, depending on the needs, one may want to use the complete data set illustrated on the top of the pyramid or use only a subset illustrated by the different branching points. Smaller subdivisions, representing groups, families, genus and species, could even be made to extend to the bottom of the pyramid. Because the tuf and atpD sequences are highly conserved and evolved with each species, the design of primers and probes does not need to include all the sequences within the database or its subdivisions. As illustrated in Annexes IV to XX, XXIII to XXXI, XXXVIII and XLII, depending on the use, sequences from a limited number of species can be carefully selected to represent: i) only the main phylogenetic branches from which the intended probes and primers need to be differentiating, and ii) only the species for which they need to be matching. However, for ubiquity purposes, and especially for primers and probes identifying large groups of species (genus, family, group or universal, or sequencing primers), the more data is included into the sequence analysis, the better the probes and primers will be suitable for each particular intended use. Similarly, for specificity purposes, a larger data set (or repertory) ensures optimal primers and probes design by reducing the chance of employing nonspecific oligonucleotides.

FIG. 3 illustrates the approach used to design specific amplification primers from fusA as well as from the region between the end of fusA and the beginning of tuf in the streptomycin (str) operon (referred to as the fusA-tuf intergenic spacer in Table 7). Shown is a schematic organization of universal amplification primers (SEQ ID NOs. 1221-1229) in the str operon. Amplicon sizes are given in bases pairs. Drawing not to scale, as the fusA-tuf intergenic spacer size varies depending on the bacterial species. Indicated amplicon lengths are for E. coli.

FIGS. 4 to 6 are illustrations to Example 42, whereas FIGS. 7 to 10 illustrate Example 43. FIGS. 11 and 12 illustrate Example 44.

FIG. 4. Abridged multiple amino acid sequence alignment of the partial tuf gene products from selected species illustrated using the program Alscript. Residues highly conserved in bacteria are boxed in grey and gaps are represented with dots. Residues in reverse print are unique to the enterococcal tufB as well as to streptococcal and lactococcal tuf gene products. Numbering is based on E. coli EF-Tu and secondary structure elements of E. coli EF-Tu are represented by cylinders (α-helices) and arrows (β-strands).

FIG. 5. Distance matrix tree of bacterial EF-Tu based on amino acid sequence homology. The tree was constructed by the neighbor-joining method. The tree was rooted using archeal and eukaryotic EF-1α genes as the outgroup. The scale bar represents 5% changes in amino acid sequence, as determined by taking the sum of all of the horizontal lines connecting two species.

FIG. 6. Southern hybridization of BglII/XbaI digested genomic DNAs of some enterococci (except for E. casseliflavus and E. gallinarum whose genomic DNA was digested with BamHI/PvuII) using the tufA gene fragment of E. faecium as probes. The sizes of hybridizing fragments are shown in kilobases. Strains tested are listed in Table 16.

FIG. 7. Pantoea and Tatumella species specific signature indel in atpD genes. The nucleotide positions given are for E. coli atpD sequence (GenBank accession no. V00267). Numbering starts from the first base of the initiation codon.

FIG. 8: Trees based on sequence data from tuf (left side) and atpD (right side). The phylogenetic analysis was performed using the Neighbor-Joining method calculated using the Kimura two-parameter method. The value on each branch indicates the occurrence (%) of the branching order in 750 bootstrapped trees.

FIG. 9: Phylogenetic tree of members of the family Enterobacteriaceae based on tuf (a), atpD (b), and 16S rDNA (c) genes. Trees were generated by neighbor-joining method calculated using the Kimura two-parameter method. The value on each branch is the percentage of bootstrap replications supporting the branch. 750 bootstrap replications were calculated.

FIG. 10: Plot of tuf distances versus 16S rDNA distances (a), atpD distances versus 16S rDNA distances (b), and atpD distances versus tuf distances (c). Symbols: ◯, distances between pairs of strains belonging to the same species; , distances between E. coli strains and Shigella strains; □, distances between pairs belonging to the same genus; ▪, distances between pairs belonging to different genera; Δ, distances between pairs belonging to different families.

FIG. 11 depicts a multiple nucleic acid sequence alignment of the vanA gene from the indicated GenBank nucleotide accession numbers. Above the alignment of the GenBank sequences is a consensus sequence, derived from the alignment of the nucleic acid sequences below. Below the alignment of the GenBank sequences and shaded in grey are the sequences of oligonucleotides (SEQ ID NOs: 1090 and 1091) and the position of a molecular beacon probe (SEQ ID NO: 2299) that hybridizes to the amplification product of SEQ ID NOs: 1090 and 1091.

FIG. 12 depicts a multiple nucleic acid sequence alignment of the vanB gene from the indicated GenBank nucleotide accession numbers. Above the alignment of the GenBank sequences is a consensus sequence, derived from the alignment of the nucleic acid sequences below. Below the alignment of the GenBank sequences and shaded in grey are the sequences of oligonucleotides (SEQ ID NOs: 1096 and 2298) and the position of a molecular beacon probe (SEQ ID NO: 2300) that hybridizes to the amplification product of SEQ ID NOs: 1096 and 2298.

FIGS. 13A and 13B shows a graphical depictions of PCR amplification curves measured from reactions containing molecular beacon probes. Reactions contained 0, 0.5, 2.5, 5. 10, or 20 copies of vanA resistant E. faecium (FIG. 13A) or vanB resistant E. faecalis (FIG. 13B) template DNA, as well as 3.5 copies of internal control DNA. Molecular beacon probes (SEQ ID NO: 2299 and 2300) were added to each reaction and the fluorescence of the reactions was measured (FIGS. 13A and 13B, respectively). SEQ ID NO: 2299 is labeled with FAM. SEQ ID NO: 2300 is labeled with Texas Red. SEQ ID NO: 2301 is labeled with TET.

FIG. 14 shows an agarose gel of the DNA amplification products from PCR using the template DNA sources listed in Table 29. The numbers above the lanes correspond to the numbers in Table 29.

FIG. 15 shows an agarose gel of the DNA amplification products from PCR using template DNA sources listed in Table 30. The numbers above the lanes correspond to the numbers in Table 30.

FIG. 16 shows an agarose gel of the DNA amplification products from PCR using template DNA sources listed in Table 31. The numbers above the lanes correspond to the numbers in Table 31.

FIG. 17 shows an agarose gel of the DNA amplification products from PCR using template DNA sources listed in Table 32. The numbers above the lanes correspond to the numbers in Table 32.

FIGS. 18A and 18B show the fluorescence signal readout obtained in the FAM channel when vanA template (FIG. 18A) or non-specific template (FIG. 18B) DNA was used in PCR according to Example 23.

FIGS. 19A and 19B show the fluorescence signal readout obtained in the TET channel when internal control (IC) template (FIG. 19A) or non-specific template (FIG. 19B) DNA was used in PCR according to Example 23

FIGS. 20A and 20B show the fluorescence signal readout obtained in the Texas Red channel when vanB template (FIG. 20A) or non-specific template (FIG. 20B) DNA was used in the PCR according to Example 23.

FIG. 21 shows the fluorescent signal readout obtained in the vanR assay for a vanA positive clinical specimen. The top panel shows the fluorescent readout from the FAM channel, and the bottom panel shows the fluorescent readout in the Texas Red channel, designed to detect the vanB probe.

FIG. 22 shows the fluorescent signal readout obtained in the vanR assay for a clinical specimen that is both vanA and vanB positive. The top panel shows the readout from the FAM channel (vanA) and the bottom panel a shows the readout from the Texas Red channel (vanB).

FIG. 23 shows the fluorescent signal readout obtained in the vanR assay for a clinical specimen that is vanB positive. The top panel shows the FAM channel (vanA) and the bottom channel shows the fluorescent readout from the Texas Red channel (vanB).

FIG. 24 shows an agarose gel of the DNA amplification products from PCR using the template DNA sources listed in Table 36. The numbers above the lanes correspond to the numbers in Table 36.

FIG. 25 shows an agarose gel of the DNA amplification products from PCR using the template DNA sources listed in Table 37. The numbers above the lanes correspond to the numbers in Table 37.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

The present inventors reasoned that comparing the published Haemophilus influenzae and Mycoplasma genitalium genomes and searching for conserved genes could provide targets to develop useful diagnostic primers and probes. This sequence comparison is highly informative as these two bacteria are distantly related and most genes present in the minimal genome of M. genitalium are likely to be present in every bacterium. Therefore genes conserved between these two bacteria are likely to be conserved in all other bacteria.

Following the genomic comparison, it was found that several protein-coding genes were conserved in evolution. Highly conserved proteins included the translation elongation factors G (EF-G) and Tu (EF-Tu) and the β subunit of F₀F₁ type ATP-synthase, and to a lesser extent, the RecA recombinase. These four proteins coding genes were selected amongst the 20 most conserved genes on the basis that they all possess at least two highly conserved regions suitable for the design of universal amplification and sequencing primers. Moreover, within the fragment amplified by these primers, highly conserved and more variable regions are also present hence suggesting it might be possible to rapidly obtain sequence information from various microbial species to design universal as well as species-, genus-, family-, or group-specific primers and probes of potential use for the detection and identification and/or quantification of microorganisms.

Translation elongation factors are members of a family of GTP-binding proteins which intervene in the interactions of tRNA molecules with the ribosome machinery during essential steps of protein synthesis. The role of elongation factor Tu is to facilitate the binding of aminoacylated tRNA molecules to the A site of the ribosome. The eukaryotic, archaeal (archaebacterial) and algal homolog of EF-Tu is called elongation factor 1 alpha (EF-1α). All protein synthesis factors originated from a common ancestor via gene duplications and fusions (Cousineau et al., 1997, J. Mol. Evol. 45:661-670). In particular, elongation factor G (EF-G), although having a functional role in promoting the translocation of aminoacyl-tRNA molecules from the A site to the P site of the ribosome, shares sequence homologies with EF-Tu and is thought to have arisen from the duplication and fusion of an ancestor of the EF-Tu gene.

In addition, EF-Tu is known to be the target for antibiotics belonging to the elfamycin's group as well as to other structural classes (Anborgh and Parmeggiani, 1991, EMBO J. 10:779-784; Luiten et al., 1992, European patent application serial No. EP 0 466 251 A1). EF-G for its part, is the target of the antibiotic fusidic acid. In addition to its crucial activities in translation, EF-Tu has chaperone-like functions in protein folding, protection against heat denaturation of proteins and interactions with unfolded proteins (Caldas et al., 1998, J. Biol. Chem 273:11478-11482). Interestingly, a form of the EF-Tu protein has been identified as a dominant component of the periplasm of Neisseria gonorrhoeae (Porcella et al., 1996, Microbiology 142:2481-2489), hence suggesting that at least in some bacterial species, EF-Tu might be an antigen with vaccine potential.

F₀F₁ type ATP-synthase belongs to a superfamily of proton-translocating ATPases divided in three major families: P, V and F (Nelson and Taiz, 1989, TIBS 14:113-116). P-ATPases (or E₁-E₂ type) operate via a phosphorylated intermediate and are not evolutionarily related to the other two families. V-ATPases (or V₀V₁ type) are present on the vacuolar and other endomembranes of eukaryotes, on the plasma membrane of archaea (archaebacteria) and algae, and also on the plasma membrane of some eubacteria especially species belonging to the order Spirochaetales as well as to the Chlamydiaceae and Deinococcaceae families. F-ATPases (or F₀F₁ type) are found on the plasma membrane of most eubacteria, on the inner membrane of mitochondria and on the thylakoid membrane of chloroplasts. They function mainly in ATP synthesis. They are large multimeric enzymes sharing numerous structural and functional features with the V-ATPases. F and V-type ATPases have diverged from a common ancestor in an event preceding the appearance of eukaryotes. The β subunit of the F-ATPases is the catalytic subunit and it possesses low but significant sequence homologies with the catalytic A subunit of V-ATPases.

The translation elongation factors EF-Tu, EF-G and EF-1α and the catalytic subunit of F or V-types ATP-synthase, are highly conserved proteins sometimes used for phylogenetic analysis and their genes are also known to be highly conserved (Iwabe et al., 1989, Proc. Natl. Acad. Sci. USA 86:9355-9359, Gogarten et al., 1989, Proc. Natl. Acad. Sci. USA 86:6661-6665, Ludwig et al., 1993, Antonie van Leeuwenhoek 64:285-305).

A recent BLAST (Altschul et al., 1997, J. Mol. Biol. 215:403-410) search performed by the present inventors on the GenBank, European Molecular Biology Laboratory (EMBL), DNA Database of Japan (DDBJ) and specific genome project databases indicated that throughout bacteria, the EF-Tu and the β subunit of F₀F₁ type ATP-synthase genes may be more conserved than other genes that are well conserved between H. influenzae and M. genitalium.

The RecA recombinase is a multifunctional protein encoded by the recA gene. It plays a central role in homologous recombination, it is critical for the repair of DNA damage and it is involved in the regulation of the SOS system by promoting the proteolytic digestion of the LexA repressor. It is highly conserved in bacteria and could serve as a useful genetic marker to reconstruct bacterial phylogeny (Miller and Kokjohn, 1990, Annu. Rev. Microbiol. 44:365-394). Although RecA possesses some highly conserved sequence segments that we used to design universal primers aimed at sequencing the recA fragments, it is clearly not as well conserved EF-G, EF-Tu and (3 subunit of F₀F₁ type ATP-synthase. Hence, RecA may not be optimal for universal detection of bacteria with high sensitivity but it was chosen because preliminary data indicated that EF-G, EF-Tu and 1 subunit of F₀F₁ type ATP-synthase may sometimes be too closely related to find specific primer pairs that could discriminate between certain very closely related species and genera. While RecA, EF-G, EF-Tu and β subunit of F₀F₁ type ATP-synthase genes, possesses highly conserved regions suitable for the design of universal sequencing primers, the less conserved region between primers should be divergent enough to allow species-specific and genus-specific primers in those cases.

Thus, as targets to design primers and probes for the genetic detection of microorganisms, the present inventors have focused on the genes encoding these four proteins: tuf, the gene for elongation factor Tu (EF-Tu); fus, the gene for the elongation factor G (EF-G); atpD, the gene for β subunit of F₀F₁ type ATP-synthase; and recA, the gene encoding the RecA recombinase. In several bacterial genomes tuf is often found in two highly similar duplicated copies named tufA and tufB (Filer and Furano, 1981, J. Bacteriol. 148:1006-1011, Sela et al., 1989, J. Bacteriol. 171:581-584). In some particular cases, more divergent copies of the tuf genes can exist in some bacterial species such as some actinomycetes (Luiten et al. European patent application publication No. EP 0 446 251 A 1; Vijgenboom et al., 1994, Microbiology 140:983-998) and, as revealed as part of this invention, in several enterococcal species. In several bacterial species, tuf is organized in an operon with its homolog gene for the elongation factor G (EF-G) encoded by the fusA gene (FIG. 3). This operon is often named the str operon. The tuf, fus, atpD and recA genes were chosen as they are well conserved in evolution and have highly conserved stretches as well as more variable segments. Moreover, these four genes have eukaryotic orthologs which are described in the present invention as targets to identify fungi and parasites. The eukaryotic homolog of elongation factor Tu is called elongation factor 1-alpha (EF-1α) (gene name: tef, tef1, ef1, ef-1 or EF-1). In fungi, the gene for EF-1α occurs sometimes in two or more highly similar duplicated copies (often named tef1, tef 2, tef3 . . . ). In addition, eukaryotes have a copy of elongation factor Tu which is originating from their organelle genome ancestry (gene name: tuf1, tufM or tufA). For the purpose of the current invention, the genes for these four functionally and evolutionarily linked elongation factors (bacterial EF-Tu and EF-G, eukaryotic EF-1α, and organellar EF-Tu) will hereafter be designated as <<tuf nucleic acids and/or sequences>>. The eukaryotic (mitochondrial) F₀F₁ type ATP-synthase beta subunit gene is named atp2 in yeast. For the purpose of the current invention, the genes of catalytic sub-unit of either F or V-type ATP-synthase will hereafter be designated as <<atpD nucleic acids and/or sequences>>. The eukaryotic homologs of RecA are distributed in two families, typified by the Rad51 and Dmc1 proteins. Archaeal homologs of RecA are called RadA. For the purpose of the current invention, the genes corresponding to the latter proteins will hereafter be designated as <<recA nucleic acids and/or sequences>>.

In the description of this invention, the terms <<nucleic acids>> and <<sequences>> might be used interchangeably. However, <<nucleic acids>> are chemical entities while <<sequences>> are the pieces of information derived from (inherent to) these <<nucleic acids>>. Both nucleic acids and sequences are equivalently valuable sources of information for the matter pertaining to this invention.

Analysis of multiple sequence alignments of tuf and atpD sequences permitted the design of oligonucleotide primers (and probes) capable of amplifying (or hybridizing to) segments of tuf (and/or fus) and atpD genes from a wide variety of bacterial species (see Examples 1 to 4, 24 and 26, and Table 7). Sequencing and amplification primer pairs for tuf nucleic acids and/or sequences are listed in Annex I and hybridization probes are listed in Annexes III and XLVII. Sequencing and amplification primer pairs for atpD nucleic acids and/or sequences are listed in Annex II. Analysis of the main subdivisions of tuf and atpD sequences (see FIGS. 1 and 2) permitted to design sequencing primers amplifying specifically each of these subdivisions. It should be noted that these sequencing primers could also be used as universal primers. However, since some of these sequencing primers include several variable sequence (degenerated) positions, their sensitivity could be lower than that of universal primers developed for diagnostic purposes. Further subdivisions could be done on the basis of the various phyla where these genes are encountered.

Similarly, analysis of multiple sequence alignments of recA sequences present in the public databases permitted the design of oligonucleotide primers capable of amplifying segments of recA genes from a wide variety of bacterial species. Sequencing and amplification primer pairs for recA sequences are listed in Annex XXI. The main subdivisions of recA nucleic acids and/or sequences comprise recA, radA, rad51 and dmc1. Further subdivisions could be done on the basis of the various phyla where these genes are encountered.

The present inventor's strategy is to get as much sequence data information from the four conserved genes (tuf, fus, atpD and recA). This ensemble of sequence data forming a repertory (with subrepertories corresponding to each target gene and their main sequence subdivisions) and then using the sequence information of the sequence repertory (or subrepertories) to design primer pairs that could permit either universal detection of algae or archaea or bacteria or fungi or parasites, detection of a family or group of microorganism (e.g. Enterobacteriaceae), detection of a genus (e.g. Streptococcus) or finally a specific species (e.g. Staphylococcus aureus). It should be noted that for the purpose of the present invention a group of microorganisms is defined depending on the needs of the particular diagnostic test. It does not need to respect a particular taxonomical grouping or phylum. See Example 12 where primers were designed to amplify a group a bacteria consisting of the 17 major bacterial species encountered as contaminants of platelet concentrates. Also remark that in that Example, the primers are not only able to sensitively and rapidly detect at least the 17 important bacterial species, but could also detect other species as well, as shown in Table 14. In these circumstances the primers shown in Example 12 are considered universal for platelet-contaminating bacteria. To develop an assay specific for the latter, one or more primers or probes specific to each species could be designed. Another example of primers and/or probes for group detection is given by the Pseudomonad group primers. These primers were designed based upon alignment of tuf sequences from real Pseudomonas species as well as from former Pseudomonas species such as Stenotrophomonas maltophilia. The resulting primers are able to amplify all Pseudomonas species tested as well as several species belonging to different genera, hence as being specific for a group including Pseudomonas and other species, we defined that group as Pseudomonads, as several members were former Pseudomonas.

For certain applications, it may be possible to develop a universal, group, family or genus-specific reaction and to proceed to species identification using sequence information within the amplicon to design species-specific internal probes or primers, or alternatively, to proceed directly by sequencing the amplicon. The various strategies will be discussed further below.

The ensembles formed by public and proprietary tuf, atpD and recA nucleic acids and/or sequences are used in a novel fashion so they constitute three databases containing useful information for the identification of microorganisms.

Sequence repertories of other gene targets were also built to solve some specific identification problems especially for microbial species genetically very similar to each other such as E. coli and Shigella (see Example 23). Based on tuf, atpD and recA sequences, Streptococcus pneumoniae is very difficult to differentiate from the closely related species S. oralis and S. mitis. Therefore, we elected to built a sequence repertory from hexA sequences (Example 19), a gene much more variable than our highly conserved tuf, atpD and recA nucleic acids and/or sequences.

For the detection of mutations associated with antibiotic resistance genes, we also built repertories to distinguish between point mutations reflecting only gene diversity and point mutations involved in resistance. This was done for pbp1a, pbp2b and pbp2x genes of penicillin-resistant and sensitive Streptococcus pneumoniae (Example 18) and also for gyrA and parC gene fragments of various bacterial species for which quinolone resistance is important to monitor.

Oligonucleotide Primers and Probes Design and Synthesis

The tuf, fus, atpD and recA DNA fragments sequenced by us and/or selected from public databases (GenBank and EMBL) were used to design oligonucleotides primers and probes for diagnostic purposes. Multiple sequence alignments were made using subsets of the tuf or atpD or recA sequences repertory. Subsets were chosen to encompass as much as possible of the targeted microorganism(s) DNA sequence data and also include sequence data from phylogenetically related microorganisms from which the targeted microorganism(s) should be distinguished. Regions suitable for primers and probes should be conserved for the targeted microorganism(s) and divergent for the microorganisms from which the targeted microorganism(s) should be distinguished. The large amount of tuf or atpD or recA sequences data in our repertory permits to reduce trial and errors in obtaining specific and ubiquitous primers and probes. We also relied on the corresponding peptide sequences of tuf, fus, atpD and recA nucleic acids and/or sequences to facilitate the identification of regions suitable for primers and probes design. As part of the design rules, all oligonucleotides (probes for hybridization and primers for DNA amplification by PCR) were evaluated for their suitability for hybridization or PCR amplification by computer analysis using standard programs (i.e. the Genetics Computer Group (GCG) programs and the primer analysis software Oligo™ 5.0). The potential suitability of the PCR primer pairs was also evaluated prior to the synthesis by verifying the absence of unwanted features such as long stretches of one nucleotide and a high proportion of G or C residues at the 3′ end (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). Oligonucleotide probes and amplification primers were synthesized using an automated DNA synthesizer (Perkin-Elmer Corp., Applied Biosystems Division).

The oligonucleotide sequence of primers or probes may be derived from either strand of the duplex DNA. The primers or probes may consist of the bases A, G, C, or T or analogs and they may be degenerated at one or more chosen nucleotide position(s). The primers or probes may be of any suitable length and may be selected anywhere within the DNA sequences from proprietary fragments or from selected database sequences which are suitable for (i) the universal detection of algae or archaea or bacteria or fungi or parasites, (ii) the species-specific detection and identification of any microorganism, including but not limited to: Abiotrophia adiacens, Bacteroides fragilis, Bordetella pertussis, Candida albicans, Candida dubliniensis, Candida glabrata, Candida guilliermondii, Candida krusei, Candida lusitaniae, Candida parapsilosis, Candida tropicalis, Candida zeylanoides, Campylobacter jejuni and C. coli, Chlamydia pneumoniae, Chlamydia trachomatis, Cryptococcus neoformans, Cryptosporidium parvum, Enterococcus faecalis, Enterococcus faecium, Enterococcus gallinarum, Escherichia coli, Haemophilus influenzae, Legionella pneumophila, Mycoplasma pneumoniae, Neisseria gonorrhoeae, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus saprophyticus, Streptococcus agalactiae, Streptococcus pneumoniae, Trypanosoma brucei, Trypanosoma cruzi, (iii) the genus-specific detection of Bordetella species, Candida species, Clostridium species, Corynebacterium species, Cryptococcus species, Entamoeba species, Enterococcus species, Gemella species, Giardia species, Legionella species, Leishmania species, Staphylococcus species, Streptococcus species, Trypanosoma species, (iv) the family-specific detection of Enterobacteriaceae family members, Mycobacteriaceae family members, Trypanosomatidae family members, (v) the detection of Enterococcus casseliflavus-flavescens-gallinarum group, Enterococcus, Gemella and Abiotrophia adiacens group, Pseudomonads extended group, Platelet-contaminating bacteria group, (vi) the detection of clinically important antimicrobial agents resistance genes listed in Table 5, (vii) the detection of clinically important toxin genes listed in Table 6.

Variants for a given target microbial gene are naturally occurring and are attributable to sequence variation within that gene during evolution (Watson et al., 1987, Molecular Biology of the Gene, 4^(th) ed., The Benjamin/Cummings Publishing Company, Menlo Park, Calif.; Lewin, 1989, Genes IV, John Wiley & Sons, New York, N.Y.). For example, different strains of the same microbial species may have a single or more nucleotide variation(s) at the oligonucleotide hybridization site. The person skilled in the art is well aware of the existence of variant algal, archaeal, bacterial, fungal or parasitical DNA nucleic acids and/or sequences for a specific gene and that the frequency of sequence variations depends on the selective pressure during evolution on a given gene product. The detection of a variant sequence for a region between two PCR primers may be demonstrated by sequencing the amplification product. In order to show the presence of sequence variants at the primer hybridization site, one has to amplify a larger DNA target with PCR primers outside that hybridization site. Sequencing of this larger fragment will allow the detection of sequence variation at this site. A similar strategy may be applied to show variants at the hybridization site of a probe. Insofar as the divergence of the target nucleic acids and/or sequences or a part thereof does not affect the specificity and ubiquity of the amplification primers or probes, variant microbial DNA is under the scope of this invention. Variants of the selected primers or probes may also be used to amplify or hybridize to a variant DNA.

Sequencing of tuf Nucleic Acids and/or Sequences from a Variety of Archaeal, Bacterial, Fungal and Parasitical Species

The nucleotide sequence of a portion of tuf nucleic acids and/or sequences was determined for a variety of archaeal, bacterial, fungal and parasitical species. The amplification primers (SEQ ID NOs. 664 and 697), which amplify a tuf gene portion of approximately 890 bp, were used along with newly designed sequencing primer pairs (See Annex I for the sequencing primers for tuf nucleic acids and/or sequences). Most primer pairs can amplify different copies of tuf genes (tufA and tufB). This is not surprising since it is known that for several bacterial species these two genes are nearly identical. For example, the entire tufA and tufB genes from E. coli differ at only 13 nucleotide positions (Neidhardt et al., 1996, Escherichia coli and Salmonella: Cellular and Molecular Biology, 2^(nd) ed., American Society for Microbiology Press, Washington, D.C.). Similarly, some fungi are known to have two nearly identical copies of tuf nucleic acids and/or sequences (EF-1□). These amplification primers are degenerated at several nucleotide positions and contain inosines in order to allow the amplification of a wide range of tuf nucleic acids and/or sequences. The strategy used to select these amplification primers is similar to that illustrated in Annex I for the selection of universal primers. The tuf sequencing primers even sometimes amplified highly divergent copies of tuf genes (tufC) as illustrated in the case of some enterococcal species (SEQ ID NOs.: 73, 75, 76, 614 to 618, 621 and 987 to 989). To prove this, we have determined the enterococcal tuf nucleic acids and/or sequences from PCR amplicons cloned into a plasmid vector. Using the sequence data from the cloned amplicons, we designed new sequencing primers specific to the divergent (tufC) copy of enterococci (SEQ ID NOs.: 658-659 and 661) and then sequenced directly the tufC amplicons. The amplification primers (SEQ ID NOs.: 543, 556, 557, 643-645, 660, 664, 694, 696 and 697) could be used to amplify the tuf nucleic acids and/or sequences from any bacterial species. The amplification primers (SEQ ID NOs.: 558, 559, 560, 653, 654, 655, 813, 815, 1974-1984, 1999-2003) could be used to amplify the tuf (EF-1 □ genes from any fungal and/or parasitical species. The amplification primers SEQ ID NOs. 1221-1228 could be used to amplify bacterial tuf nucleic acids and/or sequences of the EF-G subdivision (fusA) (FIG. 3). The amplification primers SEQ ID NOs. 1224, and 1227-1229 could be used to amplify bacterial tuf nucleic acids and/or sequences comprising the end of EF-G (fusA) and the beginning of EF-Tu (tuf), including the intergenic region, as shown in FIG. 3.

Most tuf fragments to be sequenced were amplified using the following amplification protocol: One μl of cell suspension (or of purified genomic DNA 0.1-100 ng/μl) was transferred directly to 19 μl of a PCR reaction mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 1 μM of each of the 2 primers, 200 μM of each of the four dNTPs, 0.5 unit of Taq DNA polymerase (Promega Corp., Madison, Wis.). PCR reactions were subjected to cycling using a PTC-200 thermal cycler (MJ Research Inc., Watertown, Mass.) as follows: 3 min at 94-96° C. followed by 30-45 cycles of 1 min at 95° C. for the denaturation step, 1 min at 50-55° C. for the annealing step and 1 min at 72° C. for the extension step. Subsequently, twenty microliters of the PCR-amplified mixture were resolved by electrophoresis in a 1.5% agarose gel. The amplicons were then visualized by staining with methylene blue (Flores et al., 1992, Biotechniques, 13:203-205). The size of the amplification products was estimated by comparison with a 100-bp molecular weight ladder. The band corresponding to the specific amplification product was excised from the agarose gel and purified using the QIAquick™ gel extraction kit (QIAGEN Inc., Chatsworth, Calif.). The gel-purified DNA fragment was then used directly in the sequencing protocol. Both strands of the tuf genes amplification product were sequenced by the dideoxynucleotide chain termination sequencing method by using an Applied Biosystems automated DNA sequencer (model 377) with their Big Dye™ Terminator Cycle Sequencing Ready Reaction Kit (Applied Biosystems, Foster City, Calif.). The sequencing reactions were performed by using the same amplification primers and 10 ng/100 by of the gel-purified amplicon per reaction. For the sequencing of long amplicons such as those of eukaryotic tuf (EF-1 □ nucleic acids and/or sequences, we designed internal sequencing primers (SEQ ID NOs.: 654, 655 and 813) to be able to obtain sequence data on both strands for most of the fragment length. In order to ensure that the determined sequence did not contain errors attributable to the sequencing of PCR artefacts, we have sequenced two preparations of the gel-purified tuf amplification product originating from two independent PCR amplifications. For most target microbial species, the sequences determined for both amplicon preparations were identical. In case of discrepancies, amplicons from a third independent PCR amplification were sequenced. Furthermore, the sequences of both strands were 100% complementary thereby confirming the high accuracy of the determined sequence. The tuf nucleic acids and/or sequences determined using the above strategy are described in the Sequence Listing. Table 7 gives the originating microbial species and the source for each tuf sequence in the Sequence Listing.

The alignment of the tuf sequences determined by us or selected from databases revealed clearly that the length of the sequenced portion of the tuf genes is variable. There may be insertions or deletions of several amino acids. In addition, in several fungi introns were observed. Intron nucleic acids and/or sequences are part of tuf nucleic acids and/or sequences and could be useful in the design of species-specific primers and probes. This explains why the size of the sequenced tuf amplification products was variable from one fungal species to another. Consequently, the nucleotide positions indicated on top of each of Annexes IV to XX, XXIII to XXXI, XXXVIII and XLII do not correspond for sequences having insertions or deletions.

It should also be noted that the various tuf nucleic acids and/or sequences determined by us occasionally contain base ambiguities. These degenerated nucleotides correspond to sequence variations between tufA and tufB genes (or copies of the EF-G subdivision of tuf nucleic acids and/or sequences, or copies of EF-1 □ subdivision of tuf nucleic acids and/or sequences for fungi and parasites) because the amplification primers amplify both tuf genes. These nucleotide variations were not attributable to nucleotide misincorporations by the Taq DNA polymerase because the sequence of both strands was identical and also because the sequences determined with both preparations of the gel-purified tuf amplicons obtained from two independent PCR amplifications were identical.

The Selection of Amplification Primers from Tuf Nucleic Acids and/or Sequences

The tuf sequences determined by us or selected from public databases were used to select PCR primers for universal detection of bacteria, as well as for genus-specific, species-specific family-specific or group-specific detection and identification. The strategy used to select these PCR primers was based on the analysis of multiple sequence alignments of various tuf sequences. For more details about the selection of PCR primers from tuf sequences please refer to Examples 5, 7-14, 17, 22, 24, 28, 30-31, 33, 36, and 38-40, and to Annexes VI-IX, XI-XIX and XXV.

Sequencing of atpD and recA Nucleic Acids and/or Sequences from a Variety of Archaeal, Bacterial, Fungal and Parasitical Species

The method used to obtain atpD and recA nucleic acids and/or sequences is similar to that described above for tuf nucleic acids and/or sequences.

The Selection of Amplification Primers from atpD or recA Nucleic Acids and/or Sequences

The comparison of the nucleotide sequence for the atpD or recA genes from various archaeal, bacterial, fungal and parasitical species allowed the selection of PCR primers (refer to Examples 6, 13, 29, 34 and 37, and to Annexes IV, V, X, and XX).

DNA Amplification

For DNA amplification by the widely used PCR (polymerase chain reaction) method, primer pairs were derived from proprietary DNA fragments or from database sequences. Prior to synthesis, the potential primer pairs were analyzed by using the Oligo™ 5.0 software to verify that they were good candidates for PCR amplification.

During DNA amplification by PCR, two oligonucleotide primers binding respectively to each strand of the heat-denatured target DNA from the microbial genome are used to amplify exponentially in vitro the target DNA by successive thermal cycles allowing denaturation of the DNA, annealing of the primers and synthesis of new targets at each cycle (Persing et al, 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.).

Briefly, the PCR protocols were as follows: Treated clinical specimens or standardized bacterial or fungal or parasitical suspensions (see below) or purified genomic DNA from bacteria, fungi or parasites were amplified in a 20 μl PCR reaction mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 2.5 mM MgCl₂, 0.4 μM of each primer, 200 μM of each of the four dNTPs and 0.5 unit of Taq DNA polymerase (Promega) combined with the TaqStart™ antibody (Clontech Laboratories Inc., Palo Alto, Calif.). The TaqStart™ antibody, which is a neutralizing monoclonal antibody to Taq DNA polymerase, was added to all PCR reactions to enhance the specificity and the sensitivity of the amplifications (Kellogg et al., 1994, Biotechniques 16:1134-1137). The treatment of the clinical specimens varies with the type of specimen tested, since the composition and the sensitivity level required are different for each specimen type. It consists in a rapid protocol to lyse the microbial cells and eliminate or neutralize PCR inhibitors. For amplification from bacterial or fungal or parasitical cultures or from purified genomic DNA, the samples were added directly to the PCR amplification mixture without any pre-treatment step. An internal control was derived from sequences not found in the target microorganisms or in the human genome. The internal control was integrated into all amplification reactions to verify the efficiency of the PCR assays and to ensure that significant PCR inhibition was absent. Alternatively, an internal control derived from rRNA was also useful to monitor the efficiency of microbial lysis protocols.

PCR reactions were then subjected to thermal cycling (3 min at 94-96° C. followed by 30 cycles of 1 second at 95° C. for the denaturation step and 30 seconds at 50-65° C. for the annealing-extension step) using a PTC-200 thermal cycler (MJ Research Inc.). The number of cycles performed for the PCR assays varies according to the sensitivity level required. For example, the sensitivity level required for microbial detection directly from clinical specimens is higher for blood specimens than for urine specimens because the concentration of microorganisms associated with a septicemia can be much lower than that associated with a urinary tract infection. Consequently, more sensitive PCR assays having more thermal cycles are probably required for direct detection from blood specimens. Similarly, PCR assays performed directly from bacterial or fungal or parasitical cultures may be less sensitive than PCR assays performed directly from clinical specimens because the number of target organisms is normally much lower in clinical specimens than in microbial cultures.

The person skilled in the art of DNA amplification knows the existence of other rapid amplification procedures such as ligase chain reaction (LCR), transcription-mediated amplification (TMA), self-sustained sequence replication (3SR), nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), branched DNA (bDNA), cycling probe technology (CPT), solid phase amplification (SPA), rolling circle amplification technology (RCA), solid phase RCA, anchored SDA and nuclease dependent signal amplification (NDSA) (Lee et al., 1997, Nucleic Acid Amplification Technologies: Application to Disease Diagnosis, Eaton Publishing, Boston, Mass.; Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.; Westin et al., 2000, Nat. Biotechnol. 18:199-204). The scope of this invention is not limited to the use of amplification by PCR, but rather includes the use of any rapid nucleic acid amplification method or any other procedure which may be used to increase the sensitivity and/or the rapidity of nucleic acid-based diagnostic tests. The scope of the present invention also covers the use of any nucleic acids amplification and detection technology including real-time or post-amplification detection technologies, any amplification technology combined with detection, any hybridization nucleic acid chips or arrays technologies, any amplification chips or combination of amplification and hybridization chips technologies. Detection and identification by any sequencing method is also under the scope of the present invention.

Any oligonucleotide suitable for the amplification of nucleic acids by approaches other than PCR or for DNA hybridization which are derived from the species-specific, genus-specific and universal DNA fragments as well as from selected antimicrobial agents resistance or toxin gene sequences included in this document are also under the scope of this invention.

Detection of Amplification Products

Classically, detection of amplification is performed by standard ethidium bromide-stained agarose gel electrophoresis. It is clear that other methods for the detection of specific amplification products, which may be faster and more practical for routine diagnosis, may be used. Such methods may be based on the detection of fluorescence after or during amplification. One simple method for monitoring amplified DNA is to measure its rate of formation by measuring the increase in fluorescence of intercalating agents such as ethidium bromide or SYBR® Green I (Molecular Probes). If more specific detection is required, fluorescence-based technologies can monitor the appearance of a specific product during the reaction. The use of dual-labeled fluorogenic probes such as in the TaqMan™ system (Applied Biosystems) which utilizes the 5′-3′ exonuclease activity of the Taq polymerase is a good example (Livak K. J. et al. 1995, PCR Methods Appl. 4:357-362). TaqMan™ can be performed during amplification and this “real-time” detection can be done in a single closed tube hence eliminating post-PCR sample handling and consequently preventing the risk of amplicon carryover. Several other fluorescence-based detection methods can be performed in real-time. Fluorescence resonance energy transfer (FRET) is the principle behind the use of adjacent hybridization probes (Wittwer, C. T. et al. 1997. BioTechniques 22:130-138), molecular beacons (Tyagi S. and Kramer F. R. 1996. Nature Biotechnology 14:303-308) and scorpions (Whitcomb et al. 1999. Nature Biotechnology 17:804-807). Adjacent hybridization probes are designed to be internal to the amplification primers. The 3′ end of one probe is labelled with a donor fluorophore while the 5′ end of an adjacent probe is labelled with an acceptor fluorophore. When the two probes are specifically hybridized in closed proximity (spaced by 1 to 5 nucleotides) the donor fluorophore which has been excited by an external light source emits light that is absorbed by a second acceptor that emit more fluorescence and yields a FRET signal. Molecular beacons possess a stem-and-loop structure where the loop is the probe and at the bottom of the stem a fluorescent moiety is at one end while a quenching moiety is at the other end. The beacons undergo a fluorogenic conformational change when they hybridize to their targets hence separating the fluorochrome from its quencher. The FRET principle is also used in an air thermal cycler with a built-in fluorometer (Wittwer, C. T. et al. 1997. BioTechniques 22:130-138). The amplification and detection are extremely rapid as reactions are performed in capillaries: it takes only 18 min to complete 45 cycles. Those techniques are suitable especially in the case where few pathogens are searched for. Boehringer-Roche Inc. sells the LightCycler™, and Cepheid makes the SmartCycler. These two apparatus are capable of rapid cycle PCR combined with fluorescent SYBR® Green I or FRET detection. We recently demonstrated in our laboratory, real-time detection of 10 CFU in less than 40 minutes using adjacent hybridization probes on the LightCycler™. Methods based on the detection of fluorescence are particularly promising for utilization in routine diagnosis as they are very rapid, quantitative and can be automated.

Microbial pathogens detection and identification may also be performed by solid support or liquid hybridization using species-specific internal DNA probes hybridizing to an amplification product. Such probes may be generated from any sequence from our repertory and designed to specifically hybridize to DNA amplification products which are objects of the present invention. Alternatively, the internal probes for species or genus or family or group detection and identification may be derived from the amplicons produced by a universal, family-, group-, genus- or species-specific amplification assay(s). The oligonucleotide probes may be labeled with biotin or with digoxigenin or with any other reporter molecule (for more details see below the section on hybrid capture). Hybridization on a solid support is amendable to miniaturization.

At present the oligonucleotide nucleic acid microarray technology is appealing. Currently, available low to medium density arrays (Heller et al., An integrated microelectronics hybridization system for genomic research and diagnostic applications. In: Harrison, D. J., and van den Berg, A., 1998, Micro total analysis systems '98, Kluwer Academic Publisher, Dordrecht.) could specifically capture fluorescent-labelled amplicons. Detection methods for hybridization are not limited to fluorescence; potentiometry, colorimetry and plasmon resonance are some examples of alternative detection methods. In addition to detection by hybridization, nucleic acid microarrays could be used to perform rapid sequencing by hybridization. Mass spectrometry could also be applicable for rapid identification of the amplicon or even for sequencing of the amplification products (Chiu and Cantor, 1999, Clinical Chemistry 45:1578; Berkenkamp et al., 1998, Science 281:260).

For the future of our assay format, we also consider the major challenge of molecular diagnostics tools, i.e.: integration of the major steps including sample preparation, genetic amplification, detection, data analysis and presentation (Anderson et al., Advances in integrated genetic analysis. In: Harrison, D. J., and van den Berg, A., 1998, Micro total analysis systems '98, Kluwer Academic Publisher, Dordrecht.).

To ensure PCR efficiency, glycerol, dimethyl sulfoxide (DMSO) or other related solvents can be used to increase the sensitivity of the PCR and to overcome problems associated with the amplification of a target DNA having a high GC content or forming strong secondary structures (Dieffenbach and Dveksler, 1995, PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview, N.Y.). The concentration ranges for glycerol and DMSO are 5-15% (v/v) and 3-10% (v/v), respectively. For the PCR reaction mixture, the concentration ranges for the amplification primers and MgCl₂ are 0.1-1.5 μM and 1.0-10.0 mM, respectively. Modifications of the standard PCR protocol using external and nested primers (i.e. nested PCR) or using more than one primer pair (i.e. multiplex PCR) may also be used (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). For more details about the PCR protocols and amplicon detection methods, see Examples.

Hybrid Capture and Chemiluminescence Detection of Amplification Products

Hybridization and detection of amplicons by chemiluminescence were adapted from Nikiforov et al. (1994, PCR Methods and Applications 3:285-291 and 1995, Anal. Biochem. 227:201-209) and from the DIG™ system protocol of Boehringer Mannheim. Briefly, 0.50 μl of a 25 picomoles solution of capture probe diluted in EDC {1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride) are immobilized in each well of 96-wells plates (Microlite™ 2, Dynex) by incubation overnight at room temperature. The next day, the plates are incubated with a solution of 1% BSA diluted into TNTw (10 mM Tris-HCl, pH 7.5; 150 mM NaCl; 0.05% Tween™. 20) for 1 hour at 37° C. The plates are then washed on a Wellwash Ascent™ (Labsystems) with TNTw followed by Washing Buffer (100 mM maleic acid pH7.5; 150 mM NaCl; 0.3% Tween™ 20).

The amplicons were labelled with DIG-11-dUTP during PCR using the PCR DIG Labelling Mix from Boehringer Mannheim according to the manufacturer's instructions. Hybridization of the amplicons to the capture probes is performed in triplicate at stringent temperature (generally, probes are designed to allow hybridization at 55° C., the stringent temperature) for 30 minutes in 1.5 M NaCl; 10 mM EDTA. It is followed by two washes in 2×SSC; 0.1% SDS, then by four washes in 0.1×SSC; 0.1% SDS at the stringent temperature (55° C.). Detection with 1,2 dioxetane chemiluminescent alkaline phosphatase substrates like CSPD® (Tropix Inc.) is performed according to the manufacturer's instructions but with shorter incubations times and a different antibody concentration. The plates are agitated at each step, the blocking incubation is performed for only 5 minutes, the anti-DIG-AP1 is used at a 1:1000 dilution, the incubation with antibody lasts 15 minutes, the plates are washed twice for only 5 minutes. Finally, after a 2 minutes incubation into the detection buffer, the plates are incubated 5 minutes with CSPD® at room temperature followed by a 10 minutes incubation at 37° C. without agitation. Luminous signal detection is performed on a Dynex Microtiter Plate Luminometer using RLU (Relative Light Units).

Specificity, Ubiquity and Sensitivity Tests for Oligonucleotide Primers and Probes

The specificity of oligonucleotide primers and probes was tested by amplification of DNA or by hybridization with bacterial or fungal or parasitical species selected from a panel comprising closely related species and species sharing the same anatomo-pathological site (see Annexes and Examples). All of the bacterial, fungal and parasitical species tested were likely to be pathogens associated with infections or potential contaminants which can be isolated from clinical specimens. Each target DNA could be released from microbial cells using standard chemical and/or physical treatments to lyse the cells (Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, 2^(nd) ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) or alternatively, genomic DNA purified with the GNOME™ DNA kit (Bio101, Vista, Calif.) was used. Subsequently, the DNA was subjected to amplification with the primer pairs. Specific primers or probes amplified only the target microbial species, genus, family or group.

Oligonucleotides primers found to amplify specifically the target species, genus, family or group were subsequently tested for their ubiquity by amplification (i.e. ubiquitous primers amplified efficiently most or all isolates of the target species or genus or family or group). Finally, the sensitivity of the primers or probes was determined by using 10-fold or 2-fold dilutions of purified genomic DNA from the targeted microorganism. For most assays, sensitivity levels in the range of 1-100 copies were obtained. The specificity, ubiquity and sensitivity of the PCR assays using the selected amplification primer pairs were tested either directly from cultures of microbial species or from purified microbial genomic DNA.

Probes were tested in hybrid capture assays as described above. An oligonucleotide probe was considered specific only when it hybridized solely to DNA from the species or genus or family or group from which it was selected. Oligonucleotide probes found to be specific were subsequently tested for their ubiquity (i.e. ubiquitous probes detected efficiently most or all isolates of the target species or genus or family or group) by hybridization to microbial DNAs from different clinical isolates of the species or genus or family or group of interest including ATCC reference strains. Similarly, oligonucleotide primers and probes could be derived from antimicrobial agents resistance or toxin genes which are objects of the present invention.

Reference Strains

The reference strains used to build proprietary tuf, atpD and recA sequence data subrepertories, as well as to test the amplification and hybridization assays were obtained from (i) the American Type Culture Collection (ATCC), (ii) the Laboratoire de santé publique du Québec (LSPQ), (iii) the Centers for Disease Control and Prevention (CDC), (iv) the National Culture Type Collection (NCTC) and (v) several other reference laboratories throughout the world. The identity of our reference strains was confirmed by phenotypic testing and reconfirmed by analysis of tuf, atpD and recA sequences (see Example 13).

Antimicrobial Agents Resistance Genes

Antimicrobial resistance complicates treatment and often leads to therapeutic failures. Furthermore, overuse of antibiotics inevitably leads to the emergence of microbial resistance. Our goal is to provide clinicians, in approximately one hour, the needed information to prescribe optimal treatments. Besides the rapid identification of negative clinical specimens with DNA-based tests for universal algal, archaeal, bacterial, fungal or parasitical detection and the identification of the presence of a specific pathogen in the positive specimens with species- and/or genus- and/or family- and/or group-specific DNA-based tests, clinicians also need timely information about the ability of the microbial pathogen to resist antibiotic treatments. We feel that the most efficient strategy to evaluate rapidly microbial resistance to antimicrobials is to detect directly from the clinical specimens the most common and clinically important antimicrobial agents resistance genes (i.e. DNA-based tests for the specific detection of antimicrobial agents resistance genes). Since the sequence from the most important and common antimicrobial agents resistance genes are available from public databases, our strategy is to use the sequence from a portion or from the entire resistance gene to design specific oligonucleotide primers or probes which will be used as a basis for the development of sensitive and rapid DNA-based tests. The list of each of the antimicrobial agents resistance genes selected on the basis of their clinical relevance (i.e. high incidence and importance) is given in Table 5; descriptions of the designed amplification primers and internal probes are given in Annexes XXXIV-XXXVII, XXXIX, XLV, and L-LI. Our approach is unique because the antimicrobial agents resistance genes detection and the microbial detection and identification can be performed simultaneously, or independently, or sequentially in multiplex or parallel or sequential assays under uniform PCR amplification conditions. These amplifications can also be done separately.

Toxin Genes

Toxin identification is often very important to prescribe optimal treatments. Besides the rapid identification of negative clinical specimens with DNA-based tests for universal bacterial detection and the identification of the presence of a specific pathogen in the positive specimens with species- and/or genus- and/or family- and/or group-specific DNA-based tests, clinicians sometimes need timely information about the ability of certain bacterial pathogens to produce toxins. Since the sequence from the most important and common bacterial toxin genes are available from public databases, our strategy is to use the sequence from a portion or from the entire toxin gene to design specific oligonucleotide primers or probes which will be used as a basis for the development of sensitive and rapid DNA-based tests. The list of each of the bacterial toxin genes selected on the basis of their clinical relevance (i.e. high incidence and importance) is given in Table 6; descriptions of the designed amplification primers and internal probes are given in Annexes XXII, XXXII and XXXIII. Our approach is unique because the toxin genes detection and the bacterial detection and identification can be performed simultaneously, or independently, or sequentially, in multiplex or parallel or sequential assays under uniform PCR amplification conditions. These amplifications can also be done separately.

Universal Bacterial Detection

In the routine microbiology laboratory, a high percentage of clinical specimens sent for bacterial identification are negative by culture. Testing clinical samples with universal amplification primers or universal probes to detect the presence of bacteria prior to specific identification and screening out the numerous negative specimens is thus useful as it reduces costs and may rapidly orient the clinical management of the patients. Several amplification primers and probes were therefore synthesized from highly conserved portions of bacterial sequences from the tuf, atpD and recA nucleic acids and/or sequences. The universal primers selection was based on a multiple sequence alignment constructed with sequences from our repertory.

All computer analysis of amino acid and nucleotide sequences were performed by using the GCG programs. Subsequently, optimal PCR primers for the universal amplification of bacteria were selected with the help of the Oligo™ program. The selected primers are degenerated at several nucleotide positions and contain several inosines in order to allow the amplification of all clinically relevant bacterial species. Inosine is a nucleotide analog able to specifically bind to any of the four nucleotides A, C, G or T. Degenerated oligonucleotides consist of an oligonucleotide mix having two or more of the four nucleotides A, C, G or T at the site of mismatches. The inclusion of inosine and/or of base ambiguities in the amplification primers allow mismatch tolerance thereby permitting the amplification of a wider array of target nucleotide sequences (Dieffenbach and Dveksler, 1995 PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview, N.Y.).

The amplification conditions with the universal primers are very similar to those used for the species- and genus-specific amplification assays except that the annealing temperature is slightly lower. The original universal PCR assay described in our assigned WO98/20157 (SEQ ID NOs. 23-24 of the latter application) was specific and nearly ubiquitous for the detection of bacteria. The specificity for bacteria was verified by amplifying genomic DNA isolated from the 12 fungal species as well as genomic DNA from Leishmania donovani, Saccharomyces cerevisiae and human lymphocytes. None of the above eukaryotic DNA preparations could be amplified by the universal assay, thereby suggesting that this test is specific for bacteria. The ubiquity of the universal assay was verified by amplifying genomic DNAs from 116 reference strains which represent 95 of the most clinically relevant bacterial species. These species have been selected from the bacterial species listed in Table 4. We found that at least 104 of these strains could be amplified. However, the assay could be improved since bacterial species which could not be amplified with the original tuf nucleic acids and/or sequences-based assay included species belonging to the following genera: Corynebacterium (11 species) and Stenotrophomonas (1 species). Sequencing of the tuf genes from these bacterial species and others has been performed in the scope of the present invention in order to improve the universal assay. This sequencing data has been used to select new universal primers which may be more ubiquitous and more sensitive. Also, we improved our primer and probes design strategy by taking into consideration the phylogeny observed in analysing our repertory of tuf, atpD and recA sequences. Data from each of the 3 main subrepertories (tuf, atpD and recA) was subjected to a basic phylogenic analysis using the Pileup command from version 10 of the GCG package (Genetics Computer Group, inc.). This analysis indicated the main branches or phyla reflecting the relationships between sequences. Instead of trying to design primers or probes able to hybridize to all phyla, we designed primers or probes able to hybridize to the main phyla while trying to use the largest phylum possible. This strategy should allow less degenerated primers hence improving sensitivity and by combining primers in a multiplex assay, improve ubiquity. Universal primers SEQ ID NOs. 643-645 based on tuf sequences have been designed to amplify most pathogenic bacteria except Actinomyceteae, Clostridiaceae and the Cytophaga, Flexibacter and Bacteroides phylum (pathogenic bacteria of this phylum include mostly Bacteroides, Porphyromonas and Prevotella species). Primers to fill these gaps have been designed for Actinomyceteae (SEQ ID NOs. 646-648), Clostridiaceae (SEQ ID NOs. 796-797, 808-811), and the Cytophaga, Flexibacter and Bacteroides phylum (SEQ ID NOs. 649-651), also derived from tuf nucleic acids and/or sequences. These primers sets could be used alone or in conjunction to render the universal assay more ubiquitous.

Universal primers derived from atpD sequences include SEQ ID NOs. 562-565. Combination of these primers does not amplify human DNA but should amplify almost all pathogenic bacterial species except proteobacteria belonging to the epsilon subdivision (Campylobacter and Helicobacter), the bacteria from the Cytophaga, Flexibacter and Bacteroides group and some actinomycetes and corynebacteria. By analysing atpD sequences from the latter species, primers and probes to specifically fill these gaps could be designed and used in conjunction with primers SEQ ID NOs. 562-565, also derived from atpD nucleic acids and/or sequences.

In addition, universality of the assay could be expanded by mixing atpD sequences-derived primers with tuf sequences-derived primers. Ultimately, even recA sequences-derived primers could be added to fill some gaps in the universal assay.

It is important to note that the 95 bacterial species selected to test the ubiquity of the universal assay include all of the most clinically relevant bacterial species associated with a variety of human infections acquired in the community or in hospitals (nosocomial infections). The most clinically important bacterial and fungal pathogens are listed in Tables 1 and 2.

Amino Acid Sequences Derived from tuf, atpD and recA Nucleic Acids and/or Sequences

The amino acid sequences translated from the repertory of tuf, atpD and recA nucleic acids and/or sequences are also an object of the present invention. The amino acid sequence data will be particularly useful for homology modeling of three-dimensional (3D) structure of the elongation factor Tu, elongation factor G, elongation factor 1α, ATPase subunit beta and RecA recombinase. For all these proteins, at least one structure model has been published using X-ray diffraction data from crystals. Based on those structural informations it is possible to use computer software to build 3D model structures for any other protein having peptide sequence homologies with the known structure (Greer, 1991, Methods in Enzymology, 202:239-252; Taylor, 1994, Trends Biotechnol., 12(5):154-158; Sali, 1995, Curr. Opin. Biotechnol. 6:437-451; Sanchez and Sali, 1997, Curr. Opin. Struct. Biol. 7:206-214; Fischer and Eisenberg, 1999, Curr. Opin. Struct. Biol. 9:208-211; Guex et al., 1999, Trends Biochem. Sci. 24: 364-367). Model structures of target proteins are used for the design or to predict the behavior of ligands and inhibitors such as antibiotics. Since EF-Tu and EF-G are already known as antibiotic targets (see above) and since the beta subunit of ATPase and RecA recombinase are essential to the survival of the microbial cells in natural conditions of infection, all four proteins could be considered antibiotic targets. Sequence data, especially the new data generated by us could be very useful to assist the creation of new antibiotic molecules with desired spectrum of activity. In addition, model structures could be used to improve protein function for commercial purposes such as improving antibiotic production by microbial strains or increasing biomass.

The following detailed embodiments and appended drawings are provided as illustrative examples of his invention, with no intention to limit the scope thereof.

EXAMPLES AND ANNEXES

For sake of clarity, here is a list of Examples and Annexes:

Example 1: Sequencing of bacterial atpD (F-type and V-type) gene fragments.

Example 2: Sequencing of eukaryotic atpD (F-type and V-type) gene fragments.

Example 3: Sequencing of eukaryotic tuf (EF-1) gene fragments.

Example 4: Sequencing of eukaryotic tuf (organelle origin, M) gene fragments.

Example 5: Specific detection and identification of Streptococcus agalactiae using tuf sequences.

Example 6: Specific detection and identification of Streptococcus agalactiae using atpD sequences.

Example 7: Development of a PCR assay for detection and identification of staphylococci at genus and species levels.

Example 8: Differentiating between the two closely related yeast species Candida albicans and Candida dubliniensis.

Example 9: Specific detection and identification of Entamoeba histolytica.

Example 10: Sensitive detection and identification of Chlamydia trachomatis.

Example 11: Genus-specific detection and identification of enterococci.

Example 12: Detection and identification of the major bacterial platelets contaminants using tuf sequences with a multiplex PCR test.

Example 13: The resolving power of the tuf and atpD sequences databases is comparable to the biochemical methods for bacterial identification.

Example 14: Detection of group B streptococci from clinical specimens.

Example 15: Simultaneous detection and identification of Streptococcus pyogenes and its pyrogenic exotoxin A.

Example 16: Real-time detection and identification of Shiga toxin-producing bacteria.

Example 17: Development of a PCR assay for the detection and identification of staphylococci at genus and species levels and its associated mecA gene.

Example 18: Sequencing of pbp1a, pbp2b and pbp2x genes of Streptococcus pneumoniae.

Example 19: Sequencing of hexA genes of Streptococcus species.

Example 20: Development of a multiplex PCR assay for the detection of Streptococcus pneumoniae and its penicillin resistance genes.

Example 21: Sequencing of the vancomycin resistance vanA, vanC1, vanC2 and vanC3 genes.

Example 22: Development of a PCR assay for the detection and identification of enterococci at genus and species levels and its associated resistance genes vanA and vanB.

Example 23: Development of a multiplex PCR assay for detection and identification of vancomycin-resistant Enterococcus faecalis, Enterococcus faecium, Enterococcus gallinarum, Enterococcus casseliflavus, and Enterococcus flavescens.

Example 24: Universal amplification involving the EF-G (fusA) subdivision of tuf sequences.

Example 25: DNA fragment isolation from Staphylococcus saprophyticus by arbitrarily primed PCR.

Example 26: Sequencing of prokaryotic tuf gene fragments.

Example 27: Sequencing of procaryotic recA gene fragments.

Example 28: Specific detection and identification of Escherichia coli/Shigella sp. using tuf sequences.

Example 29: Specific detection and identification of Klebsiella pneumoniae using atpD sequences.

Example 30: Specific detection and identification of Acinetobacter baumanii using tuf sequences.

Example 31: Specific detection and identification of Neisseria gonorrhoeae using tuf sequences.

Example 32: Sequencing of bacterial gyrA and parC gene fragments.

Example 33: Development of a PCR assay for the specific detection and identification of Staphylococcus aureus and its quinolone resistance genes gyrA and parC.

Example 34: Development of a PCR assay for the detection and identification of Klebsiella pneumoniae and its quinolone resistance genes gyrA and parC.

Example 35: Development of a PCR assay for the detection and identification of Streptococcus pneumoniae and its quinolone resistance genes gyrA and parC.

Example 36: Detection of extended-spectrum TEM-type β-lactamases in Escherichia coli.

Example 37: Detection of extended-spectrum SHV-type β-lactamases in Klebsiella pneumoniae.

Example 38: Development of a PCR assay for the detection and identification of Neisseria gonorrhoeae and its associated tetracycline resistance gene tetM.

Example 39: Development of a PCR assay for the detection and identification of Shigella sp. and their associated trimethoprim resistance gene dhfrIa.

Example 40: Development of a PCR assay for the detection and identification of Acinetobacter baumanii and its associated aminoglycoside resistance gene aph(3′)-VIa.

Example 41: Specific detection and identification of Bacteroides fragilis using atpD (V-type) sequences.

Example 42: Evidence for horizontal gene transfer in the evolution of the elongation factor Tu in Enterococci.

Example 43: Elongation factor Tu (tuf) and the F-ATPase beta-subunit (atpD) as phylogenetic tools for species of the family Enterobacteriaceae.

Example 44: Testing new pairs of PCR primers selected from two species-specific genomic DNA fragments which are objects of U.S. Pat. No. 6,001,564.

Example 45: Testing modified versions of PCR primers derived from the sequence of several primers which are objects of U.S. Pat. No. 6,001,564.

The various Annexes show the strategies used for the selection of a variety of DNA amplification primers, nucleic acid hybridization probes and molecular beacon internal probes:

-   -   (i) Annex I shows the amplification primers used for nucleic         acid amplification from tuf sequences.     -   (ii) Annex II shows the amplification primers used for nucleic         acid amplification from atpD sequences.     -   (iii) Annex III shows the internal hybridization probes for         detection of tuf sequences.     -   (iv) Annex IV illustrates the strategy used for the selection of         the amplification primers specific for atpD sequences of the         F-type.     -   (v) Annex V illustrates the strategy used for the selection of         the amplification primers specific for atpD sequences of the         V-type.     -   (vi) Annex VI illustrates the strategy used for the selection of         the amplification primers specific for the tuf sequences of         organelle lineage (M, the letter M is used to indicate that in         most cases, the organelle is the mitochondria).     -   (vii) Annex VII illustrates the strategy used for the selection         of the amplification primers specific for the tuf sequences of         eukaryotes (EF-1).     -   (viii) Annex VIII illustrates the strategy for the selection of         Streptococcus agalactiae-specific amplification primers from tuf         sequences.     -   (ix) Annex IX illustrates the strategy for the selection of         Streptococcus agalactiae-specific hybridization probes from tuf         sequences.     -   (x) Annex X illustrates the strategy for the selection of         Streptococcus agalactiae-specific amplification primers from         atpD sequences.     -   (xi) Annex XI illustrates the strategy for the selection from         tuf sequences of Candida albicans/dubliniensis-specific         amplification primers, Candida albicans-specific hybridization         probe and Candida dubliniensis-specific hybridization probe.     -   (xii) Annex XII illustrates the strategy for the selection of         Staphylococcus-specific amplification primers from tuf         sequences.     -   (xiii) Annex XIII illustrates the strategy for the selection of         the Staphylococcus-specific hybridization probe from tuf         sequences.     -   (xiv) Annex XIV illustrates the strategy for the selection of         Staphylococcus saprophyticus-specific and Staphylococcus         haemolyticus-specific hybridization probes from tuf sequences.     -   (xv) Annex XV illustrates the strategy for the selection of         Staphylococcus aureus-specific and Staphylococcus         epidermidis-specific hybridization probes from tuf sequences.     -   (xvi) Annex XVI illustrates the strategy for the selection of         the Staphylococcus hominis-specific hybridization probe from tuf         sequences.     -   (xvii) Annex XVII illustrates the strategy for the selection of         the Enterococcus-specific amplification primers from tuf         sequences.     -   (xviii) Annex XVIII illustrates the strategy for the selection         of the Enterococcus faecalis-specific hybridization probe, of         the Enterococcus faecium-specific hybridization probe and of the         Enterococcus casseliflavus-flavescens-gallinarum group-specific         hybridization probe from tuf sequences.     -   (xix) Annex XIX illustrates the strategy for the selection of         primers from tuf sequences for the identification of platelets         contaminants.     -   (xx) Annex XX illustrates the strategy for the selection of the         universal amplification primers from atpD sequences.     -   (xxi) Annex XXI shows the amplification primers used for nucleic         acid amplification from recA sequences.     -   (xxii) Annex XXII shows the specific and ubiquitous primers for         nucleic acid amplification from speA sequences.     -   (xxiii) Annex XXIII illustrates the first strategy for the         selection of Streptococcus pyogenes-specific amplification         primers from speA sequences.     -   (xxiv) Annex XXIV illustrates the second strategy for the         selection of Streptococcus pyogenes-specific amplification         primers from speA sequences.     -   (xxv) Annex XXV illustrates the strategy for the selection of         Streptococcus pyogenes-specific amplification primers from tuf         sequences.     -   (xxvi) Annex XXVI illustrates the strategy for the selection of         stx₁-specific amplification primers and hybridization probe.     -   (xxvii) Annex XXVII illustrates the strategy for the selection         of stx₂-specific amplification primers and hybridization probe.     -   (xxviii) Annex XXVIII illustrates the strategy for the selection         of vanA-specific amplification primers from van sequences.     -   (xxix) Annex XXIX illustrates the strategy for the selection of         vanB-specific amplification primers from van sequences.     -   (xxx) Annex XXX illustrates the strategy for the selection of         vanC-specific amplification primers from vanC sequences.     -   (xxxi) Annex XXXI illustrates the strategy for the selection of         Streptococcus pneumoniae-specific amplification primers and         hybridization probes from pbp1a sequences.     -   (xxxii) Annex XXXII shows the specific and ubiquitous primers         for nucleic acid amplification from toxin gene sequences.     -   (xxxiii) Annex XXXIII shows the molecular beacon internal         hybridization probes for specific detection of toxin sequences.     -   (xxxiv) Annex XXXIV shows the specific and ubiquitous primers         for nucleic acid amplification from van sequences.     -   (xxxv) Annex XXXV shows the internal hybridization probes for         specific detection of van sequences.     -   (xxxvi) Annex XXXVI shows the specific and ubiquitous primers         for nucleic acid amplification from pbp sequences.     -   (xxxvii) Annex XXXVII shows the internal hybridization probes         for specific detection of pbp sequences.     -   (xxxviii) Annex XXXVIII illustrates the strategy for the         selection of vanAB-specific amplification primers and vanA- and         vanB-specific hybridization probes from van sequences.     -   (xxxix) Annex XXXIX shows the internal hybridization probe for         specific detection of mecA.     -   (xl) Annex XL shows the specific and ubiquitous primers for         nucleic acid amplification from hexA sequences.     -   (xli) Annex XLI shows the internal hybridization probe for         specific detection of hexA.     -   (xlii) Annex XLII illustrates the strategy for the selection of         Streptococcus pneumoniae species-specific amplification primers         and hybridization probe from hexA sequences.     -   (xliii) Annex XLIII shows the specific and ubiquitous primers         for nucleic acid amplification from pcp sequences.     -   (xliv) Annex XLIV shows specific and ubiquitous primers for         nucleic acid amplification of S. saprophyticus sequences of         unknown coding potential.     -   (xlv) Annex XLV shows the molecular beacon internal         hybridization probes for specific detection of antimicrobial         agents resistance gene sequences.     -   (xlvi) Annex XLVI shows the molecular beacon internal         hybridization probe for specific detection of S. aureus gene         sequences of unknown coding potential.     -   (xlvii) Annex XLVII shows the molecular beacon hybridization         internal probe for specific detection of tuf sequences.     -   (xlviii) Annex XLVIII shows the molecular beacon internal         hybridization probes for specific detection of ddI and mtl         sequences.     -   (xlix) Annex XLIX shows the internal hybridization probe for         specific detection of S. aureus sequences of unknown coding         potential.     -   (l) Annex L shows the amplification primers used for nucleic         acid amplification from antimicrobial agents resistance genes         sequences.     -   (li) Annex LI shows the internal hybridization probes for         specific detection of antimicrobial agents resistance genes         sequences.     -   (lii) Annex LII shows the molecular beacon internal         hybridization probes for specific detection of atpD sequences.     -   (liii) Annex LIII shows the internal hybridization probes for         specific detection of atpD sequences.     -   (liv) Annex LIVI shows the internal hybridization probes for         specific detection of ddI and mtl sequences.

As shown in these Annexes, the selected amplification primers may contain inosines and/or base ambiguities. Inosine is a nucleotide analog able to specifically bind to any of the four nucleotides A, C, G or T. Alternatively, degenerated oligonucleotides which consist of an oligonucleotide mix having two or more of the four nucleotides A, C, G or T at the site of mismatches were used. The inclusion of inosine and/or of degeneracies in the amplification primers allows mismatch tolerance thereby permitting the amplification of a wider array of target nucleotide sequences (Dieffenbach and Dveksler, 1995 PCR Primer: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Plainview, N.Y.).

EXAMPLES Example 1 Sequencing of Bacterial atpD (F-Type and V-Type) Gene Fragments

As shown in Annex IV, the comparison of publicly available atpD (F-type) sequences from a variety of bacterial species revealed conserved regions allowing the design of PCR primers able to amplify atpD sequences (F-type) from a wide range of bacterial species. Using primers pairs SEQ ID NOs. 566 and 567, 566 and 814, 568 and 567, 570 and 567, 572 and 567, 569 and 567, 571 and 567, 700 and 567, it was possible to amplify and sequence atpD sequences SEQ ID NOs. 242-270, 272-398, 673-674, 737-767, 866-867, 942-955, 1245-1254, 1256-1265, 1527, 1576, 1577, 1600-1604, 1640-1646, 1649, 1652, 1655, 1657, 1659-1660, 1671, 1844-1845, and 1849-1865.

Similarly, Annex V shows the strategy to design the PCR primers able to amplify atpD sequences of the V-type from a wide range of archaeal and bacterial species. Using primers SEQ ID NOs. 681-683, it was possible to amplify and sequence atpD sequences SEQ ID NOs. 827-832, 929-931, 958 and 966. As the gene was difficult to amplify for several species, additional amplification primers were designed inside the original amplicon (SEQ ID NOs. 1203-1207) in order to obtain sequence information for these species. Other primers (SEQ ID NO. 1212, 1213, 2282-2285) were also designed to amplify regions of the atpD gene (V-type) in archaebacteria.

Example 2 Sequencing of Eukaryotic atpD (F-Type and V-Type) Gene Fragments

The comparison of publicly available atpD (F-type) sequences from a variety of fungal and parasitical species revealed conserved regions allowing the design of PCR primers able to amplify atpD sequences from a wide range of fungal and parasitical species. Using primers pairs SEQ ID NOs. 568 and 573, 574 and 573, 574 and 708, and 566 and 567, it was possible to amplify and sequence atpD sequences SEQ ID NOs. 458-497, 530-538, 663, 667, 676, 678-680, 768-778, 856-862, 889-896, 941, 1638-1639, 1647, 1650-1651, 1653-1654, 1656, 1658, 1684, 1846-1848, and 2189-2192.

In the same manner, the primers described in Annex V (SEQ ID NOs. 681-683) could amplify the atpD (V-type) gene from various fungal and parasitical species. This strategy allowed to obtain SEQ ID NOs. 834-839, 956-957, and 959-965.

Example 3 Sequencing of Eukaryotic tuf (EF-1) Gene Fragments

As shown in Annex VII, the comparison of publicly available tuf (EF-1) sequences from a variety of fungal and parasitical species revealed conserved regions allowing the design of PCR primers able to amplify tuf sequences from a wide range of fungal and parasitical species. Using primers pairs SEQ ID NOs. 558 and 559, 813 and 559, 558 and 815, 560 and 559, 653 and 559, 558 and 655, and 654 and 559, 1999 and 2000, 2001 and 2003, 2002 and 2003, it was possible to amplify and sequence tuf sequences SEQ ID NOs. 399-457, 509-529, 622-624, 677, 779-790, 840-842, 865, 897-903, 1266-1287, 1561-1571 and 1685.

Example 4 Sequencing of Eukaryotic tuf (Organelle Origin, M) Gene Fragments

As shown in Annex VI, the comparison of publicly available tuf (organelle origin, M) sequences from a variety of fungal and parasitical organelles revealed conserved regions allowing the design of PCR primers able to amplify tuf sequences of several organelles belonging to a wide range fungal and parasitical species. Using primers pairs SEQ ID NOs. 664 and 652, 664 and 561, 911 and 914, 912 and 914, 913 and 915, 916 and 561, 664 and 917, it was possible to amplify and sequence tuf sequences SEQ ID NOs. 498-508, 791-792, 843-855, 904-910, 1664, 1666-1667, 1669-1670, 1673-1683, 1686-1689, 1874-1876, 1879, 1956-1960, and 2193-2199.

Example 5 Specific Detection and Identification of Streptococcus agalactiae Using tuf Sequences

As shown in Annex VIII, the comparison of tuf sequences from a variety of bacterial species allowed the selection of PCR primers specific for S. agalactiae. The strategy used to design the PCR primers was based on the analysis of a multiple sequence alignment of various tuf sequences. The multiple sequence alignment includes the tuf sequences of four bacterial strains from the target species as well as tuf sequences from other species and bacterial genera, especially representatives of closely related species. A careful analysis of this alignment allowed the selection of oligonucleotide sequences which are conserved within the target species but which discriminate sequences from other species and genera, especially from the closely related species, thereby permitting the species-specific, ubiquitous and sensitive detection and identification of the target bacterial species.

The chosen primer pair, oligos SEQ ID NO. 549 and SEQ ID NO. 550, gives an amplification product of 252 bp. Standard PCR was carried out using 0.4 μM of each primer, 2.5 mM MgCl₂, BSA 0.05 mM, 1× Taq Buffer (Promega), dNTP 0.2 mM (Pharmacia), 0.5 U Taq DNA polymerase (Promega) coupled with TaqStart™ antibody (Clontech Laboratories Inc., Palo Alto), 1 μl of genomic DNA sample in a final volume of 20 μl using a PTC-200 thermocycler (MJ Research Inc.). The optimal cycling conditions for maximum sensitivity and specificity were 3 minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 62° C., followed by terminal extension at 72° C. for 2 minutes. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide.

Specificity of the assay was tested by adding into the PCR reactions, 0.1 ng of genomic DNA from each of the bacterial species listed in Table 8. Efficient amplification was observed only for the 5 S. agalactiae strains listed. Of the other bacterial species, including 32 species representative of the vaginal flora and 27 other streptococcal species, only S. acidominimus yielded amplification. The signal with 0.1 ng of S. acidominimus genomic DNA was weak and the detection limit for this species was 10 pg (corresponding to more than 4000 genome copies) while the detection limit for S. agalactiae was 2.5 fg (corresponding to one genome copy) of genomic DNA.

To increase the specificity of the assay, internal probes were designed for FRET (Fluorescence Resonance Energy Transfer) detection using the LightCycler™ (Idaho Technology). As illustrated in Annex IX, a multiple sequence alignment of streptococcal tuf sequence fragments corresponding to the 252 by region amplified by primers SEQ ID NO. 549 and SEQ ID NO. 550, was used for the design of internal probes TSagHF436 (SEQ ID NO. 582) and TSagHF465 (SEQ ID NO. 583). The region of the amplicon selected for internal probes contained sequences unique and specific to S. agalactiae. SEQ ID NO. 583, the more specific probe, is labelled with fluorescein in 3′, while SEQ ID NO. 582, the less discriminant probe, is labelled with CY5 in 5′ and blocked in 3′ with a phosphate group. However, since the FRET signal is only emitted if both probes are adjacently hybridized on the same target amplicon, detection is highly specific.

Real-time detection of PCR products using the LightCycler™ was carried out using 0.4 μM of each primer (SEQ ID NO. 549-550), 0.2 μM of each probe (SEQ ID NO. 582-583), 2.5 mM MgCl₂, BSA 450 μg/ml, 1×PC2 Buffer (AB Peptides, St-Louis, dNTP 0.2 mM (Pharmacia), 0.5 U KlenTaq1™ DNA polymerase (AB Peptides) coupled with TaqStart™ antibody (Clontech Laboratories Inc., Palo Alto), 0.7 μl of genomic DNA sample in a final volume of 7 μl using a LightCycler thermocycler (Idaho Technology). The optimal cycling conditions for maximum sensitivity and specificity were 3 minutes at 94° C. for initial denaturation, then forty cycles of three steps consisting of 0 second (this setting meaning the LightCycler will reach the target temperature and stay at it for its minimal amount of time) at 94° C., 10 seconds at 64° C., 20 seconds at 72° C. Amplification was monitored during each annealing steps using the fluorescence ratio. The streptococcal species having close sequence homologies with the tuf sequence of S. agalactiae (S. acidominimus, S. anginosus, S. bovis, S. dysgalactiae, S. equi, S. ferus, S. gordonii, S. intermedius, S. parasanguis, S. parauberis, S. salivarius, S. sanguis, S. suis) as well as S. agalactiae were tested in the LightCycler with 0.07 ng of genomic DNA per reaction. Only S. agalactiae yielded an amplification signal, hence demonstrating that the assay is species-specific. With the LightCycler™ assay using the internal FRET probes, the detection limit for S. agalactiae was 1-2 genome copies of genomic DNA.

Example 6 Specific Detection and Identification of Streptococcus agalactiae Using atpD Sequences

As shown in Annex X, the comparison of atpD sequences from a variety of bacterial species allowed the selection of PCR primers specific for S. agalactiae. The primer design strategy is similar to the strategy described in the preceding Example except that atpD sequences were used in the alignment.

Four primers were selected, ASag42 (SEQ ID NO. 627), ASag52 (SEQ ID NO. 628), ASag206 (SEQ ID NO. 625) and ASag371 (SEQ ID NO. 626). The following combinations of these four primers give four amplicons; SEQ ID NO. 627+SEQ ID NO. 625=190 bp, SEQ ID NO. 628+SEQ ID NO. 625=180 bp, SEQ ID NO. 627+SEQ ID NO. 626=355 bp, and SEQ ID NO. 628+SEQ ID NO. 626=345 bp.

Standard PCR was carried out on PTC-200 thermocyclers (MJ Research Inc) using 0.4 μM of each primers pair, 2.5 mM MgCl₂, BSA 0.05 mM, 1× taq Buffer (Promega), dNTP 0.2 mM (Pharmacia), 0.5 U Taq DNA polymerase (Promega) coupled with TaqStart™ antibody (Clontech Laboratories Inc., Palo Alto), 1 μl of genomic DNA sample in a final volume of 20 μL. The optimal cycling conditions for maximum sensitivity and specificity were adjusted for each primer pair. Three minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at the optimal annealing temperature specified below were followed by terminal extension at 72° C. for 2 minutes. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide. Since atpD sequences are relatively more specific than tuf sequences, only the most closely related species namely, the streptococcal species listed in Table 9, were tested.

All four primer pairs only amplified the six S. agalactiae strains. With an annealing temperature of 63° C., the primer pair SEQ ID NO. 627+SEQ ID NO. 625 had a sensitivity of 1-5 fg (equivalent to 1-2 genome copies). At 55° C., the primer pair SEQ ID NO. 628+SEQ ID NO. 625 had a sensitivity of 2.5 fg (equivalent to 1 genome copy). At 60° C., the primer pair SEQ ID NO. 627+SEQ ID NO. 626 had a sensitivity of 10 fg (equivalent to 4 genome copies). At 58° C., the primer pair SEQ ID NO. 628+SEQ ID NO. 626 had a sensitivity of 2.5-5 fg (equivalent to 1-2 genome copies). This proves that all four primer pairs can detect S. agalactiae with high specificity and sensitivity. Together with Example 5, this example demonstrates that both tuf and atpD sequences are suitable and flexible targets for the identification of microorganisms at the species level. The fact that 4 different primer pairs based on atpD sequences led to efficient and specific amplification of S. agalactiae demonstrates that the challenge is to find target genes suitable for diagnostic purposes, rather than finding primer pairs from these target sequences.

Example 7 Development of a PCR Assay for Detection and Identification of Staphylococci at Genus and Species Levels Materials and Methods

Bacterial strains. The specificity of the PCR assay was verified by using a panel of ATCC (America Type Culture Collection) and DSMZ (Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH; German Collection of Microorganisms and Cell Cultures) reference strains consisting of 33 gram-negative and 47 gram-positive bacterial species (Table 12). In addition, 295 clinical isolates representing 11 different species of staphylococci from the microbiology laboratory of the Centre Hospitalier Universitaire de Québec, Pavillon Centre Hospitalier de l'Université Laval (CHUL) (Step-Foy, Québec, Canada) were also tested to further validate the Staphylococcus-specific PCR assay. These strains were all identified by using (i) conventional methods or (ii) the automated MicroScan Autoscan-4 system equipped with the Positive BP Combo Panel Type 6 (Dade Diagnostics, Mississauga, Ontario, Canada). Bacterial strains from frozen stocks kept at −80° C. in brain heart infusion (BHI) broth containing 10% glycerol were cultured on sheep blood agar or in BHI broth (Quelab Laboratories Inc, Montréal, Québec, Canada).

PCR primers and internal probes. Based on multiple sequence alignments, regions of the tuf gene unique to staphylococci were identified. Staphylococcus-specific PCR primers TStaG422 (SEQ ID NO. 553) and TStaG765 (SEQ ID NO. 575) were derived from these regions (Annex XII). These PCR primers are displaced by two nucleotide positions compared to original Staphylococcus-specific PCR primers described in our patent publication WO98/20157 (SEQ ID NOs. 17 and 20 in the said patent publication). These modifications were done to ensure specificity and ubiquity of the primer pair, in the light of new tuf sequence data revealed in the present patent application for several additional staphylococcal species and strains.

Similarly, sequence alignment analysis were performed to design genus and species-specific internal probes (see Annexes XIII to XVI). Two internal probes specific for Staphylococcus (SEQ ID NOs. 605-606), five specific for S. aureus (SEQ ID NOs. 584-588), five specific for S. epidermidis (SEQ ID NO. 589-593), two specific for S. haemolyticus (SEQ ID NOs. 594-595), three specific for S. hominis (SEQ ID NOs. 596-598), four specific for S. saprophyticus (SEQ ID NOs. 599-601 and 695), and two specific for coagulase-negative Staphylococcus species including S. epidermidis, S. hominis, S. saprophyticus, S. auricularis, S. capitis, S. haemolyticus, S. lugdunensis, S. simulans, S. cohnii and S. warneri (SEQ ID NOs. 1175-1176) were designed. The range of mismatches between the Staphylococcus-specific 371-bp amplicon and each of the 20-mer species-specific internal probes was from 1 to 5, in the middle of the probe when possible. No mismatches were present in the two Staphylococcus-specific probes for the 11 species analyzed: S. aureus, S. auricularis, S. capitis, S. cohnii, S. epidermidis, S. haemolyticus, S. hominis, S. lugdunensis, S. saprophyticus, S. simulans and S. warneri. In order to verify the intra-specific sequence conservation of the nucleotide sequence, sequences were obtained for the 371-bp amplicon from five unrelated ATCC and clinical strains for each of the species S. aureus, S. epidermidis, S. haemolyticus, S. hominis and S. saprophyticus. The Oligo™ (version 5.0) primer analysis software (National Biosciences, Plymouth, Minn.) was used to confirm the absence of self-complementary regions within and between the primers or probes. When required, the primers contained inosines or degenerated nucleotides at one or more variable positions. Oligonucleotide primers and probes were synthesized on a model 394 DNA synthesizer (Applied Biosystems, Mississauga, Ontario, Canada). Detection of the hybridization was performed with the DIG-labeled dUTP incorporated during amplification with the Staphylococcus-specific PCR assay, and the hybridization signal was detected with a luminometer (Dynex Technologies) as described above in the section on luminescent detection of amplification products. Annexes XIII to XVI illustrate the strategy for the selection of several internal probes.

PCR amplification. For all bacterial species, amplification was performed from purified genomic DNA or from a bacterial suspension whose turbidity was adjusted to that of a 0.5 McFarland standard, which corresponds to approximately 1.5×10⁸ bacteria per ml. One nanogram of genomic DNA or 1 □l of the standardized bacterial suspension was transferred directly to a 19 □l PCR mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 0.2 □M (each) of the two Staphylococcus genus-specific primers (SEQ ID NOs. 553 and 575), 200 □M (each) of the four deoxynucleoside triphosphates (Pharmacia Biotech), 3.3 □g/□l bovine serum albumin (BSA) (Sigma-Aldrich Canada Ltd, Oakville, Ontario, Canada), and 0.5 U Taq polymerase (Promega) coupled with TaqStart™ Antibody (Clontech). The PCR amplification was performed as follows: 3 min. at 94° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 55° C., plus a terminal extension at 72° C. for 2 minutes. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide. Visualization of the PCR products was made under UV at 254 nm.

For determination of the sensitivities of the PCR assays, two-fold dilutions of purified genomic DNA were used to determine the minimal number of genome copies which can be detected.

Results

Amplifications with the Staphylococcus genus-specific PCR assay. The specificity of the assay was assessed by performing 30-cycle and 40-cycle PCR amplifications with the panel of gram-positive (47 species from 8 genera) and gram-negative (33 species from 22 genera) bacterial species listed in Table 12. The PCR assay was able to detect efficiently 27 of 27 staphylococcal species tested in both 30-cycle and 40-cycle regimens. For 30-cycle PCR, all bacterial species tested other than staphylococci were negative. For 40-cycle PCR, Enterococcus faecalis and Macrococcus caseolyticus were slightly positive for the Staphylococcus-specific PCR assay. The other species tested remained negative. Ubiquity tests performed on a collection of 295 clinical isolates provided by the microbiology laboratory of the Centre Hospitalier Universitaire de Québec, Pavillon Centre Hospitalier de l'Université Laval (CHUL), including Staphylococcus aureus (n=34), S. auricularis (n=2), S. capitis (n=19), S. cohnii (n=5), S. epidermidis (n=18), S. haemolyticus (n=21), S. hominis (n=73), S. lugdunensis (n=17), S. saprophyticus (n=6), S. simulans (n=3), S. warneri (n=32) and Staphylococcus sp. (n=65), showed a uniform amplification signal with the 30-cycle PCR assays and a perfect relation between the genotype and classical identification schemes.

The sensitivity of the Staphylococcus-specific assay with 30-cycle and 40-cycle PCR protocols was determined by using purified genomic DNA from the 11 staphylococcal species previously mentioned. For PCR with 30 cycles, a detection limit of 50 copies of genomic DNA was consistently obtained. In order to enhance the sensitivity of the assay, the number of cycles was increased. For 40-cycle PCR assays, the detection limit was lowered to a range of 5-10 genome copies, depending on the staphylococcal species tested.

Hybridization between the Staphylococcus-specific 371-bp amplicon and species-specific or genus-specific internal probes. Inter-species polymorphism was sufficient to generate species-specific internal probes for each of the principal species involved in human diseases (S. aureus, S. epidermidis, S. haemolyticus, S. hominis and S. saprophyticus). In order to verify the intra-species sequence conservation of the nucleotide sequence, sequence comparisons were performed on the 371-bp amplicon from five unrelated ATCC and clinical strains for each of the 5 principal staphylococcal species: S. aureus, S. epidermidis, S. haemolyticus, S. hominis and S. saprophyticus. Results showed a high level of conservation of nucleotide sequence between different unrelated strains from the same species. This sequence information allowed the development of staphylococcal species identification assays using species-specific internal probes hybridizing to the 371-bp amplicon. These assays are specific and ubiquitous for those five staphylococcal species. In addition to the species-specific internal probes, the genus-specific internals probes were able to recognize all or most Staphylococcus species tested.

Example 8 Differentiating Between the Two Closely Related Yeast Species Candida albicans and Candida dubliniensis

It is often useful for the clinician to be able to differentiate between two very closely related species of microorganisms. Candida albicans is the most important cause of invasive human mycose. In recent years, a very closely related species, Candida dubliniensis, was isolated in immunosuppressed patients. These two species are difficult to distinguish by classic biochemical methods. This example demonstrates the use of tuf sequences to differentiate Candida albicans and Candida dubliniensis. PCR primers SEQ ID NOs. 11-12, from previous patent publication WO98/20157, were selected for their ability to specifically amplify a tuf (elongation factor 1 alpha type) fragment from both species (see Annex XI for primer positions). Within this tuf fragment, a region differentiating C. albicans and C. dubliniensis by two nucleotides was selected and used to design two internal probes (see Annex XI for probe design, SEQ ID NOs. 577 and 578) specific for each species. Amplification of genomic DNA from C. albicans and C. dubliniensis was carried out using DIG-11-dUTP as described above in the section on chemiluminescent detection of amplification products. Internal probes SEQ ID NOs. 577 and 578 were immobilized on the bottom of individual microtiter plates and hybridization was carried out as described above in the above section on chemiluminescent detection of amplification products. Luminometer data showed that the amplicon from C. albicans hybridized only to probe SEQ ID NO. 577 while the amplicon from C. dubliniensis hybridized only to probe SEQ ID NO. 578, thereby demonstrating that each probe was species-specific.

Example 9 Specific Identification of Entamoeba histolytica

Upon analysis of tuf (elongation factor 1 alpha) sequence data, it was possible to find four regions where Entamoeba histolytica sequences remained conserved while other parasitical and eukaryotic species have diverged. Primers TEntG38 (SEQ ID NO. 703), TEntG442 (SEQ ID NO. 704), TEntG534 (SEQ ID NO. 705), and TEntG768 (SEQ ID NO. 706) were designed so that SEQ ID NO. 703 could be paired with the three other primers. On PTC-200 thermocyclers (MJ Research), the cycling conditions for initial sensitivity and specificity testing were 3 min. at 94° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 55° C., followed by terminal extension at 72° C. for 2 minutes. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide. The three primer pairs could detect the equivalent of less than 200 E. histolytica genome copies. Specificity was tested using 0.5 ng of purified genomic DNA from a panel of microorganisms including Babesia bovis, Babesia microtti, Candida albicans, Crithidia fasciculata, Leishmania major, Leishmania hertigi and Neospora caninum. Only E. histolytica DNA could be amplified, thereby suggesting that the assay was species-specific.

Example 10 Sensitive Identification of Chlamydia trachomatis

Upon analysis of tuf sequence data, it was possible to find two regions where Chlamydia trachomatis sequences remained conserved while other species have diverged. Primers Ctr82 (SEQ ID NO. 554) and Ctr249 (SEQ ID NO. 555) were designed. With the PTC-200 thermocyclers (MJ Research), the optimal cycling conditions for maximum sensitivity and specificity were determined to be 3 min. at 94° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 60° C., followed by terminal extension at 72° C. for 2 minutes. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide. The assay could detect the equivalent of 8 C. trachomatis genome copies. Specificity was tested with 0.1 ng of purified genomic DNA from a panel of microorganisms including 22 species commonly encountered in the vaginal flora (Bacillus subtilis, Bacteroides fragilis, Candida albicans, Clostridium difficile, Corynebacterium cervicis, Corynebacterium urealyticum, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, Fusobacterium nucleatum, Gardnerella vaginalis, Haemophilus influenzae, Klebsiella oxytoca, Lactobacillus acidophilus, Peptococcus niger, Peptostreptococcus prevotii, Porphyromonas asaccharolytica, Prevotella melaminogenica, Propionibacterium acnes, Staphylococcus aureus, Streptococcus acidominimus, and Streptococcus agalactiae). Only C. trachomatis DNA could be amplified, thereby suggesting that the assay was species-specific.

Example 11 Genus-Specific Detection and Identification of Enterococci

Upon analysis of tuf sequence data and comparison with the repertory of tuf sequences, it was possible to find two regions where Enterococcus sequences remained conserved while other genera have diverged (Annex XVII). Primer pair Encg313dF and Encg599c (SEQ ID NOs. 1137 and 1136) was tested for its specificity by using purified genomic DNA from a panel of bacteria listed in Table 10. Using the PTC-200 thermocycler (MJ Research), the optimal cycling conditions for maximum sensitivity and specificity were determined to be 3 min. at 94° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 55° C., followed by terminal extension at 72° C. for 2 minutes. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide. Visualization of the PCR products was made under UV at 254 nm. The 18 enterococcal species listed in Table 10 were all amplified efficiently. The only other species amplified were Abiotrophia adiacens, Gemella haemolysans and Gemella morbillorum, three gram-positive species. Sensitivity tested with several strains of E. casseliflavus, E. faecium, E. faecalis, E. flavescens and E. gallinarum and with one strain of each other Enterococcus species listed in Table 10 ranged from 1 to 10 copies of genomic DNA. The sequence variation within the 308-bp amplicon was sufficient so that internal probes could be used to speciate the amplicon and differentiate enterococci from Abiotrophia adiacens, Gemella haemolysans and Gemella morbillorum, thereby allowing to achieve excellent specificity. Species-specific internal probes were generated for each of the clinically important species, E. faecalis (SEQ ID NO. 1174), E. faecium (SEQ ID NO. 602), and the group including E. casseliflavus, E. flavescens and E. gallinarum (SEQ ID NO. 1122) (Annex XVIII). The species-specific internal probes were able to differentiate their respective Enterococcus species from all other Enterococcus species. These assays are sensitive, specific and ubiquitous for those five Enterococcus species.

Example 12 Identification of the Major Bacterial Platelets Contaminants Using Tuf Sequences with a Multiplex PCR Test

Blood platelets preparations need to be monitored for bacterial contaminations. The tuf sequences of 17 important bacterial contaminants of platelets were aligned. As shown in Annex XIX, analysis of these sequences allowed the design of PCR primers. Since in the case of contamination of platelet concentrates, detecting all species (not just the more frequently encountered ones) is desirable, perfect specificity of primers was not an issue in the design. However, sensitivity is important. That is why, to avoid having to put too much degeneracy, only the most frequent contaminants were included in primer design, knowing that the selected primers would anyway be able to amplify more species than the 17 used in the design because they target highly conserved regions of tuf sequences. Oligonucleotide sequences which are conserved in these 17 major bacterial contaminants of platelet concentrates were chosen (oligos Tplaq 769 and Tplaq 991, respectively SEQ ID NOs. 636 and 637) thereby permitting the detection of these bacterial species. However, sensitivity was slightly deficient with staphylococci. To ensure maximal sensitivity in the detection of all the more frequent bacterial contaminants, a multiplex assay also including oligonucleotide primers targeting the Staphylococcus genera (oligos Stag 422, SEQ ID NO. 553; and Stag 765, SEQ ID NO. 575) was developed. The bacterial species detected with the assay are listed in Table 14.

The primer pairs, oligos SEQ ID NO. 636 and SEQ ID NO. 637 that give an amplification product of 245 pb, and oligos SEQ ID NO. 553 and SEQ ID NO. 575 that give an amplification product of 368 pb, were used simultaneously in the multiplex PCR assay. Detection of these PCR products was made on the LightCycler thermocycler (Idaho Technology) using SYBR® Green I (Molecular Probe Inc.). SYBR® Green I is a fluorescent dye that binds specifically to double-stranded DNA.

Fluorogenic detection of PCR products with the LightCycler was carried out using 1.0 μM of both Tplaq primers (SEQ ID NOs. 636-637) and 0.4 μM of both TStaG primers (SEQ ID NOs. 553 and 575), 2.5 mM MgCl₂, BSA 7.5 μM, dNTP 0.2 mM (Pharmacia), 10 mM Tris-HCl (pH 8.3), 50 mM KCl, 0.5 U Taq DNA polymerase (Boerhinger Mannheim) coupled with TaqStart™ antibody (Clontech), and 0.07 ng of genomic DNA sample in a final volume of 7 μl. The optimal cycling conditions for maximum sensitivity and specificity were 1 minute at 94° C. for initial denaturation, then forty-five cycles of three steps consisting of 0 second at 95° C., 5 seconds at 60° C. and 9 seconds at 72° C. Amplification was monitored during each elongation cycle by measuring the level of SYBR® Green I. However, real analysis takes place after PCR. Melting curves are done for each sample and transformation of the melting peak allows determination of Tm. Thus primer-dimer and specific PCR product are discriminated. With this assay, all prominent bacterial contaminants of platelet concentrates listed in Annex XIX and Table 14 were detected. Sensitivity tests were performed on the 9 most frequent bacterial contaminants of platelets. The detection limit was less than 20 genome copies for E. cloacae, B. cereus, S. choleraesuis and S. marcescens; less than 15 genome copies for P. aeruginosa; and 2 to 3 copies were detected for S. aureus, S. epidermidis, E. coli and K. pneumoniae. Further refinements of assay conditions should increase sensitivity levels.

Example 13 The Resolving Power of the tuf and atpD Sequences Databases is Comparable to the Biochemical Methods for Bacterial Identification

The present gold standard for bacterial identification is mainly based on key morphological traits and batteries of biochemical tests. Here we demonstrate that the use of tuf and atpD sequences combined with simple phylogenetic analysis of databases formed by these sequences is comparable to the gold standard. In the process of acquiring data for the tuf sequences, we sequenced the tuf gene of a strain that was given to us labelled as Staphylococcus hominis ATCC 35982. That tuf sequence (SEQ ID NO. 192) was incorporated into the tuf sequences database and subjected to a basic phylogenic analysis using the Pileup command from version 10 of the GCG package (Genetics Computer Group). This analysis indicated that SEQ ID NO. 192 is not associated with other S. hominis strains but rather with the S. warneri strains. The ATCC 35982 strain was sent to the reference laboratory of the Laboratoire de santé publique du Québec (LSPQ). They used the classic identification scheme for staphylococci (Kloos and Schleifer, 1975., J. Clin. Microbiol. 1:82-88). Their results shown that although the colonial morphology could correspond to S. hominis, the more precise biochemical assays did not. These assays included discriminant mannitol, mannose and ribose acidification tests as well as rapid and dense growth in deep thioglycolate agar. The LSPQ report identified strain ATCC 35982 as S. warneri which confirms our database analysis. The same thing happened for S. warneri (SEQ ID NO. 187) which had initially been identified as S. haemolyticus by a routine clinical laboratory using a low resolving power automated system (MicroScan, AutoScan-4™). Again, the tuf and LSPQ analysis agreed on its identification as S. warneri. In numerous other instances, in the course of acquiring tuf and atpD sequence data from various species and genera, analysis of our tuf and/or atpD sequence databases permitted the exact identification of mislabeled or erroneously identified strains. These results clearly demonstrate the usefulness and the high resolving power of our sequence-based identification assays using the tuf and atpD sequences databases.

Example 14 Detection of Group B Streptococci from Clinical Specimens Introduction

Streptococcus agalactiae, the group B streptococcus (GBS), is responsible for a severe illness affecting neonate infants. The bacterium is passed from the healthy carrier mother to the baby during delivery. To prevent this infection, it is recommended to treat expectant mothers susceptible of carrying GBS in their vaginal/anal flora. Carrier status is often a transient condition and rigorous monitoring requires cultures and classic bacterial identification weeks before delivery. To improve the detection and identification of GBS we developed a rapid, specific and sensitive PCR test fast enough to be performed right at delivery.

Materials and Methods

GBS clinical specimens. A total of 66 duplicate vaginal/anal swabs were collected from 41 consenting pregnant women admitted for delivery at the Centre Hospitalier Universitaire de Québec, Pavillon Saint-Francois d'Assise following the CDC recommendations. The samples were obtained either before or after rupture of membranes. The swab samples were tested at the Centre de Recherche en Infectiologie de l'Université Laval within 24 hours of collection. Upon receipt, one swab was cut and then the tip of the swab was added to GNS selective broth for identification of group B streptococci (GBS) by the standard culture methods recommended by the CDC. The other swab was processed following the instruction of the IDI DNA extraction kit (Infectio Diagnotics (IDI) Inc.) prior to PCR amplification.

Oligonucleotides. PCR primers, Tsag340 (SEQ ID NO. 549) and Tsag552 (SEQ ID NO. 550) complementary to the regions of the tuf gene unique for GBS were designed based upon a multiple sequence alignment using our repertory of tuf sequences. Oligo primer analysis software (version 5.0) (National Biosciences) was used to analyse primers annealing temperature, secondary structure potential as well as mispriming and dimerization potential. The primers were synthesized using a model 391 DNA synthesizer (Applied Biosystems).

A pair of fluorescently labeled adjacent hybridization probes Sag465-F (SEQ ID NO. 583) and Sag436-C (SEQ ID NO. 582) were synthesized and purified by Operon Technologies. They were designed to meet the recommendations of the manufacturer (Idaho Technology) and based upon multiple sequence alignment analysis using our repertory of tuf sequences to be specific and ubiquitous for GBS. These adjacent probes, which are separated by one nucleotide, allow fluorescence resonance energy transfer (FRET), generating an increased fluorescence signal when both hybridized simultaneously to their target sequences. The probe SEQ ID NO. 583 was labeled with FITC in 3 prime while SEQ ID NO. 582 was labeled with Cy5 in 5 prime. The Cy5-labeled probes contained a 3′-blocking phosphate group to prevent extension of the probes during the PCR reactions.

PCR amplification. Conventional amplifications were performed either from 2 μl of a purified genomic DNA preparation or cell lysates of vaginal/anal specimens. The 20 μl PCR mixture contained 0.4 μM of each GBS-specific primer (SEQ ID NOs. 549-550), 200 μM of each deoxyribonucleotide (Pharmacia Biotech), 10 mM Tris-HCl (pH 9.0), 50 mM KCl, 0.1% Triton X-100, 2.5 mM MgCl₂, 3.3 mg/ml bovine serum albumin (BSA) (Sigma), and 0.5 U of Taq polymerase (Promega) combined with the TaqStart™ antibody (Clontech). The TaqStart™ antibody, which is a neutralizing monoclonal antibody of Taq DNA polymerase, was added to all PCR reactions to enhance the efficiency of the amplification. The PCR mixtures were subjected to thermal cycling (3 min at 95° C. and then 40 cycles of 1 s at 95° C., and 30 s at 62° C. with a 2-min final extension at 72° C.) with a PTC-200 DNA Engine thermocycler (MJ research). The PCR-amplified reaction mixture was resolved by agarose gel electrophoresis.

The LightCycler™ PCR amplifications were performed with 1 μl of a purified genomic DNA preparation or cell lysates of vaginal/anal specimens. The 10 μl amplification mixture consisted of 0.4 μM each GBS-specific primer (SEQ ID NOs. 549-550), 200 μM each dNTP, 0.2 μM each fluorescently labeled probe (SEQ ID NOs. 582-583), 300 μg/ml BSA (Sigma), and 1 μl of 10×PC2 buffer (containing 50 mM Tris-HCl (pH 9.1), 16 mM ammonium sulfate, 3.5 mM Mg²⁺, and 150 μg/ml BSA) and 0.5 U KlenTaq1™ (AB Peptides) coupled with TaqStart™ antibody (Clontech). KlenTaq1™ is a highly active and more heat-stable DNA polymerase without 5′-exonuclease activity. This prevents hydrolysis of hybridized probes by the 5′ to 3′ exonuclease activity. A volume of 7 μl of the PCR mixture was transferred into a composite capillary tube (Idaho Technology). The tubes were then centrifuged to move the reaction mixture to the tips of the capillaries and then cleaned with optical-grade methanol. Subsequently the capillaries were loaded into the carousel of a LC32 LightCycler™ (Idaho Technology), an instrument that combines rapid-cycle PCR with fluorescence analysis for continuous monitoring during amplification. The PCR reaction mixtures were subjected to a denaturation step at 94° C. for 3 min followed by 45 cycles of 0 s at 94° C., 20 s at 64° C. and 10 s at 72° C. with a temperature transition rate of 20° C./s. Fluorescence signals were obtained at each cycle by sequentially positioning each capillary on the carousel at the focus of optical elements affiliated to the built-in fluorimeter for 100 milliseconds. Complete amplification and analysis required about 35 min.

Specificity and sensitivity tests. The specificity of the conventional and LightCycler™ PCR assays was verified by using purified genomic DNA (0.1 ng/reaction) from a battery of ATCC reference strains representing 35 clinically relevant gram-positive species (Abiotrophia defectiva ATCC 49176, Bifidobacterium breve ATCC 15700, Clostridium difficile ATCC 9689, Corynebacterium urealyticum ATCC 43042, Enterococcus casseliflavus ATCC 25788, Enterococcus durans ATCC 19432, Enterococcus faecalis ATCC 29212, Enterococcus faecium ATCC 19434, Enterococcus gallinarum ATCC 49573, Enterococcus raffinosus ATCC 49427, Lactobacillus reuteri ATCC 23273, Lactococcus lactis ATCC 19435, Listeria monocytogenes ATCC 15313, Peptococcus niger ATCC 27731, Peptostreptococcus anaerobius ATCC 27337, Peptostreptococcus prevotii ATCC 9321, Staphylococcus aureus ATCC 25923, Staphylococcus epidermidis ATCC 14990, Staphylococcus haemolyticus ATCC 29970, Staphylococcus saprophyticus ATCC 15305, Streptococcus agalactiae ATCC 27591, Streptococcus anginosus ATCC 33397, Streptococcus bovis ATCC 33317, Streptococcus constellatus ATCC 27823, Streptococcus dysgalactiae ATCC 43078, Streptococcus gordonii ATCC 10558, Streptococcus mitis ATCC 33399, Streptococcus mutans ATCC 25175, Streptococcus oralis ATCC 35037, Streptococcus parauberis ATCC 6631, Streptococcus pneumoniae ATCC 6303, Streptococcus pyogenes ATCC 19615, Streptococcus salivarius ATCC 7073, Streptococcus sanguinis ATCC 10556, Streptococcus uberis ATCC 19436). These microbial species included 15 species of streptococci and many members of the normal vaginal and anal floras. In addition, 40 GBS isolates of human origin, whose identification was confirmed by a latex agglutination test (Streptex, Murex), were also used to evaluate the ubiquity of the assay.

For determination of the sensitivities (i.e., the minimal number of genome copies that could be detected) for conventional and LightCycler™ PCR assays, serial 10-fold or 2-fold dilutions of purified genomic DNA from 5 GBS ATCC strains were used. Results

Evaluation of the GBS-specific conventional and LightCycler™ PCR assays. The specificity of the two assays demonstrated that only DNAs from GBS strains could be amplified. Both PCR assays did not amplify DNAs from any other bacterial species tested including 14 streptococcal species other than GBS as well as phylogenetically related species belonging to the genera Enterococcus, Peptostreptococcus and Lactococcus. Important members of the vaginal or anal flora, including coagulase-negative staphylococci, Lactobacillus sp., and Bacteriodes sp. were also negative with the GBS-specific PCR assay. The LightCycler™ PCR assays detected only GBS DNA by producing an increased fluorescence signal which was interpreted as a positive PCR result. Both PCR methods were able to amplify all of 40 GBS clinical isolates, showing a perfect correlation with the phenotypic identification methods.

The sensitivity of the assay was determined by using purified genomic DNA from the 5 ATCC strains of GBS. The detection limit for all of these 5 strains was one genome copy of GBS. The detection limit of the assay with the LightCycler™ was 3.5 fg of genomic DNA (corresponding to 1-2 genome copies of GBS). These results confirmed the high sensitivity of our GBS-specific PCR assay.

Direct Detection of GBS from vaginal/anal specimens. Among 66 vaginal/anal specimens tested, 11 were positive for GBS by both culture and PCR. There was one sample positive by culture only. The sensitivity of both PCR methods with vaginal/anal specimens for identifying colonization status in pregnant women at delivery was 91.7% when compared to culture results. The specificity and positive predictive values were both 100% and the negative predictive value was 97.8%. The time for obtaining results was approximately 45 min for LightCycler™ PCR, approximately 100 min for conventional PCR and 48 hours for culture.

Conclusion

We have developed two PCR assays (conventional and LightCycler™) for the detection of GBS, which are specific (i.e., no amplification of DNA from a variety of bacterial species other than GBS) and sensitive (i.e., able to detect around 1 genome copy for several reference ATCC strains of GBS). Both PCR assays are able to detect GBS directly from vaginal/anal specimens in a very short turnaround time. Using the real-time PCR assay on LightCycler™, we can detect GBS carriage in pregnant women at delivery within 45 minutes.

Example 15 Simultaneous Detection and Identification of Streptococcus pyogenes and its Pyrogenic Exotoxin A

The rapid detection of Streptococcus pyogenes and of its pyrogenic exotoxin A is of clinical importance. We developed a multiplex assay which permits the detection of strains of S. pyogenes carrying the pyrogenic toxin A gene, which is associated with scarlet fever and other pathologies. In order to specifically detect S. pyogenes, nucleotide sequences of the pyrrolidone carboxylyl peptidase (pcp) gene were aligned to design PCR primers Spy291 (SEQ ID NO. 1211) and Spy473 (SEQ ID NO. 1210). Next, we designed primers for the specific detection of the pyrogenic exotoxin A. Nucleotide sequences of the speA gene, carried on the bacteriophage T12, were aligned as shown in Annex XXIII to design PCR primers Spytx814 (SEQ ID NO. 994) and Spytx 927 (SEQ ID NO. 995).

The primer pairs: oligos SEQ ID NOs. 1210-1211, yielding an amplification product of 207 bp, and oligos SEQ ID NOs. 994-995, yielding an amplification product of 135 bp, were used in a multiplex PCR assay.

PCR amplification was carried out using 0.4 μM of both pairs of primers, 2.5 mM MgCl₂, BSA 0.05 μM, dNTP 0.2 μM (Pharmacia), 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 0.5 U Taq DNA polymerase (Promega) coupled with TaqStart™ antibody (Clontech Laboratories Inc.), and 1 μl of genomic DNA sample in a final volume of 20 PCR amplification was performed using a PTC-200 thermal cycler (MJ Research). The optimal cycling conditions for maximum specificity and sensitivity were 3 minutes at 94° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 63° C., followed by a final step of 2 minutes at 72° C. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide. Visualization of the PCR products was made under UV at 254 nm.

The detection limit was less than 5 genome copies for both S. pyogenes and its pyrogenic exotoxin A. The assay was specific for pyrogenic exotoxin A-producing S. pyogenes: strains of the 27 other species of Streptococcus tested, as well as 20 strains of various gram-positive and gram-negative bacterial species were all negative.

A similar approach was used to design an alternative set of speA-specific primers (SEQ ID NOs. 996 to 998, see Annex XXIV). In addition, another set of primers based on the tuf gene (SEQ ID NOs. 999 to 1001, see Annex XXV) could be used to specifically detect Streptococcus pyogenes.

Example 16 Real-Time Detection and Identification of Shiga Toxin-Producing Bacteria

Shiga toxin-producing Escherichia coli and Shigella dysenteriae cause bloody diarrhea. Currently, identification relies mainly on the phenotypic identification of S. dysenteriae and E. coli serotype O157:H7. However, other serotypes of E. coli are increasingly found to be producers of type 1 and/or type 2 Shiga toxins. Two pairs of PCR primers targeting highly conserved regions present in each of the Shiga toxin genes stx₁ and stx₂ were designed to amplify all variants of those genes (see Annexes XXVI and XXVII). The first primer pair, oligonucleotides 1SLT224 (SEQ ID NO. 1081) and 1SLT385 (SEQ ID NO. 1080), yields an amplification product of 186 by from the six, gene. For this amplicon, the 1SLTB1-Fam (SEQ ID NO. 1084) molecular beacon was designed for the specific detection of six, using the fluorescent label 6-carboxy-fluorescein. The 1 SltS1-FAM (SEQ ID NO. 2012) molecular scorpion was also designed as an alternate way for the specific detection of stx₁. A second pair of PCR primers, oligonucleotides 2SLT537 (SEQ ID NO. 1078) and 2SLT678b (SEQ ID NO. 1079), yields an amplification product of 160 by from the stx₂ gene. Molecular beacon 2SLTB1-Tet (SEQ ID NO. 1085) was designed for the specific detection of stx₂ using the fluorescent label 5-tetrachloro-fluorescein. Both primer pairs were combined in a multiplex PCR assay.

PCR amplification was carried out using 0.8 μM of primer pair SEQ ID NOs. 1080-1081, 0.5 μM of primer pair SEQ ID NOs. 1078-1079, 0.3 μM of each molecular beacon, 8 mM MgCl₂, 490 μg/mL BSA, 0.2 mM dNTPs (Pharmacia), 50 mM Tris-HCl, 16 mM NH₄SO₄, 1× TaqMaster (Eppendorf), 2.5 U KlenTaq1 DNA polymerase (AB Peptides) coupled with TaqStart™ antibody (Clontech Laboratories Inc.), and 1 μl of genomic DNA sample in a final volume of 25 PCR amplification was performed using a SmartCycler thermal cycler (Cepheid). The optimal cycling conditions for maximum sensitivity and specificity were 60 seconds at 95° C. for initial denaturation, then 45 cycles of three steps consisting of 10 seconds at 95° C., 15 seconds at 56° C. and 5 seconds at 72° C. Detection of the PCR products was made in real-time by measuring the fluorescent signal emitted by the molecular beacon when it hybridizes to its target at the end of the annealing step at 56° C.

The detection limit was the equivalent of less than 5 genome copies. The assay was specific for the detection of both toxins, as demonstrated by the perfect correlation between PCR results and the phenotypic characterization performed using antibodies specific for each Shiga toxin type. The assay was successfully performed on several Shiga toxin-producing strains isolated from various geographic areas of the world, including 10 O157:H7 E. coli, 5 non-O157:H7 E. coli and 4 S. dysenteriae.

Example 17 Development of a PCR Assay for the Detection and Identification of Staphylococci at Genus and Species Levels and its Associated mecA Gene

The Staphylococcus-specific PCR primers described in Example 7 (SEQ ID NOs. 553 and 575) were used in multiplex with the mecA-specific PCR primers and the S. aureus-specific primers described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NOs. 261 and 262 for mecA and SEQ ID NOs. 152 and 153 for S. aureus in the said patent). Sequence alignment analysis of 10 publicly available mecA gene sequences allowed to design an internal probe specific to mecA (SEQ ID NO. 1177). An internal probe was also designed for the S. aureus-specific amplicon (SEQ ID NO 1234). PCR amplification and agarose gel electrophoresis of the amplified products were performed as described in Example 7, with the exception that 0.4 μM (each) of the two Staphylococcus-specific primers (SEQ ID NOs. 553 and 575) and 0.4 μM (each) of the mecA-specific primers and 0.4 μM (each) of the S. aureus-specific primers were used in the PCR mixture. The specificity of the multiplex assay with 40-cycle PCR protocols was verified by using purified genomic DNA from five methicillin-resistant and fifteen methicillin-sensitive staphylococcal strains. The sensitivity of the multiplex assay with 40-cycle PCR protocols was determined by using purified genomic DNA from twenty-three methicillin-resistant and twenty-eight methicillin-sensitive staphylococcal strains. The detection limit was 2 to 10 genome copies of genomic DNA, depending on the staphylococcal species tested. Furthermore, the mecA-specific internal probe, the S. aureus-specific internal probe and the coagulase-negative staphylococci-specific internal probe (described in Example 7) were able to recognize twenty-three methicillin-resistant staphylococcal strains and twenty-eight methicillin-sensitive staphylococcal strains with high sensitivity and specificity.

The format of the assay is not limited to the one described above. A person skilled in the art could adapt the assay for different formats such as PCR with real-time detection using molecular beacon probes. Molecular beacon probes designed to be used in this assay include, but are not limited to, SEQ ID NO. 1232 for detection of the S. aureus-specific amplicon, SEQ ID NO. 1233 for detection of coagulase-negative staphylococci and SEQ ID NO. 1231 for detection of mecA.

Alternatively, a multiplex PCR assay containing the Staphylococcus-specific PCR primers described in Example 7 (SEQ ID NOs. 553 and 575) and the mecA-specific PCR primers described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NOs. 261 and 262 in the said patent) were developed. PCR amplification and agarose gel electrophoresis of the amplified products were performed as described in Example 7, with the exception that 0.4 μM (each) of the Staphylococcus-specific primers (SEQ ID NOs. 553 and 575) and 0.4 μM (each) of the mecA-specific primers described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NOs. 261 and 262 in the said patent) were used in the PCR mixture. The sensitivity of the multiplex assay with 40-cycle PCR protocols was determined by using purified genomic DNA from two methicillin-resistant and five methicillin-sensitive staphylococcal strains. The detection limit was 2 to 5 copies of genomic DNA, depending on the staphylococcal species tested. The specificity of the multiplex PCR assay coupled with capture-probe hybridization was tested with two strains of methicillin-resistant S. aureus, two strains of methicillin-sensitive S. aureus and seven strains of methicillin-sensitive coagulase-negative staphylococci. The mecA-specific internal probe (SEQ ID NO. 1177) and the S. aureus-specific internal probe (SEQ ID NO. 587) described in Example 7 were able to recognize all the strains with high specificity showing a perfect correlation with susceptibility to methicillin. The sensitivity of the PCR assay coupled with capture-probe hybridization was tested with one strain of methicillin-resistant S. aureus. The detection limit was around 10 copies of genomic DNA.

Example 18 Sequencing of pbp1a, pbp2b and pbp2x Genes of Streptococcus pneumoniae

Penicillin resistance in Streptococcus pneumoniae involves the sequential alteration of up to five penicillin-binding proteins (PBPs) 1A, 1B, 2A, 2X and 2B in such a way that their affinity is greatly reduce toward the antibiotic molecule. The altered PBP genes have arisen as the result of interspecies recombination events from related streptococcal species. Among the PBPs usually found in S. pneumoniae, PBPs 1A, 2B, and 2X play the most important role in the development of penicillin resistance. Alterations in PBP 2B and 2X mediate low-level resistance to penicillin while additional alterations in PBP 1A plays a significant role in full penicillin resistance.

In order to generate a database for pbp sequences that can be used for design of primers and/or probes for the specific and ubiquitous detection of β-lactam resistance in S. pneumoniae, pbp1a, pbp2b and pbp2x DNA fragments sequenced by us or selected from public databases (GenBank and EMBL) from a variety of S. pneumoniae strains were used to design oligonucleotide primers. This database is essential for the design of specific and ubiquitous primers and/or probes for detection of β-lactam resistance in S. pneumoniae since the altered PBP 1A, PBP 2B and PBP 2X of β-lactam resistant S. pneumoniae are encoded by mosaic genes with numerous sequence variations among resistant isolates. The PCR primers were located in conserved regions of pbp genes and were able to amplify pbp1a, pbp2b, and pbp2x sequences of several strains of S. pneumoniae having various levels of resistance to penicillin and third-generation cephalosporins. Using primer pairs SEQ ID NOs. 1125 and 1126, SEQ ID NOs. 1142 and 1143, SEQ ID NOs. 1146 and 1147, it was possible to amplify and determine pbp1a sequences SEQ ID NOs. 1004-1018, 1648, 2056-2060 and 2062-2064, pbp2b sequences SEQ ID NOs. 1019-1033, and pbp2x sequences SEQ ID NOs. 1034-1048. Six other PCR primers (SEQ ID NOs. 1127-1128, 1144-1145, 1148-1149) were also designed and used to complete the sequencing of pbp1a, pbp2b and pbp2x amplification products. The described primers (SEQ ID NOs. 1125 and 1126, SEQ ID NOs. 1142 and 1143, SEQ ID NOs. 1146 and 1147, SEQ ID NOs. 1127-1128, 1144-1145, 1148-1149) represent a powerful tool for generating new pbp sequences for design of primers and/or probes for detection of β-lactam resistance in S. pneumoniae.

Example 19 Sequencing of hexA Genes of Streptococcus Species

The hexA sequence of S. pneumoniae described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NO. 31 in the said patent, SEQ ID NO. 1183 in the present application) allowed the design of a PCR primer (SEQ ID NO. 1182) which was used with primer Spn1401 described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NO. 156 in the said patent, SEQ ID NO. 1179 in the present application) to generate a database for hexA sequences that can be used to design primers and/or probes for the specific identification and detection of S. pneumoniae (Annex XLII). Using primers SEQ ID NO. 1179 and SEQ ID NO. 1182 (Annex XLII), it was possible to amplify and determine the hexA sequence from S. pneumoniae (4 strains) (SEQ ID NOs. 1184-1187), S. mitis (three strains) (SEQ ID NOs. 1189-1191) and S. oralis (SEQ ID NO. 1188).

Example 20 Development of Multiplex PCR Assays Coupled with Capture Probe Hybridization for the Detection and Identification of Streptococcus pneumoniae and its Penicillin Resistance Genes

Two different assays were developed to identify S. pneumoniae and its susceptibility to penicillin.

Assay I:

Bacterial strains. The specificity of the multiplex PCR assay was verified by using a panel of ATCC (American Type Culture Collection) reference strains consisting of 33 gram-negative and 67 gram-positive bacterial species (Table 13). In addition, a total of 98 strains of S. pneumoniae, 16 strains of S. mitis and 3 strains of S. oralis from the American Type Culture Collection, the microbiology laboratory of the Centre Hospitalier Universitaire de Québec, Pavillon Centre Hospitalier de l'Université Laval (CHUL), (Step-Foy, Québec, Canada), the Laboratoire de santé publique du Québec, (Sainte-Anne-de-Bellevue, Québec, Canada), the Sunnybrook and Women's College Health Sciences Centre (Toronto, Canada), the Infectious Diseases Section, Department of Veterans Affairs Medical Center, (Houston, USA) were also tested to further validate the Streptococcus pneumoniae-specific PCR assay. The penicillin MICs (minimal inhibitory concentrations) were measured by the broth dilution method according to the recommended protocol of NCCLS.

PCR primers and internal probes. The analysis of hexA sequences from a variety of streptococcal species from the publicly available hexA sequence and from the database described in Example 19 (SEQ ID NOs. 1184-1191) allowed the selection of a PCR primer specific to S. pneumoniae, SEQ ID NO. 1181. This primer was used with the S. pneumoniae-specific primer SEQ ID NO. 1179 to generate an amplification product of 241 by (Annex XLII). The PCR primer SEQ ID NO. 1181 is located 127 nucleotides downstream on the hexA sequence compared to the original S. pneumoniae-specific PCR primer Spn1515 described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NO. 157 in the said patent). These modifications were done to ensure the design of the S. pneumoniae-specific internal probe according to the new hexA sequences of several streptococcal species from the database described in Example 19 (SEQ ID NOs. 1184-1191).

The analysis of pbp1a sequences from S. pneumoniae strains with various levels of penicillin resistance from public databases and from the database described in Example 18 allowed the identification of amino acid substitutions Ile-459 to Met and Ser-462 to Ala that occur in isolates with high-level penicillin resistance (MICs≧1 μg/ml), and amino acid substitutions Ser-575 to Thr, Gln-576 to Gly and Phe-577 to Tyr that are common to all penicillin-resistant isolates with MICs≧0.25 μg/ml. As shown in Annex XXXI, PCR primer pair SEQ ID NOs. 1130 and 1131 were designed to detect high-level penicillin resistance (MICs≧1 μg/ml), whereas PCR primer pair SEQ ID NOs. 1129 and 1131 were designed to detect intermediate- and high-level penicillin resistance (MICs≧0.25 μg/ml).

The analysis of hexA sequences from the publicly available hexA sequence and from the database described in Example 19 allowed the design of an internal probe specific to S. pneumoniae (SEQ ID NO. 1180) (Annex XLII). The range of mismatches between the S. pneumoniae-specific 241-bp amplicon was from 2 to 5, in the middle of the 19-bp probe. The analysis of pbp1a sequences from public databases and from the database described in Example 18 allowed the design of five internal probes containing all possible mutations to detect the high-level penicillin resistance 383-bp amplicon (SEQ ID NOs. 1197, 1217-1220). Alternatively, two other internal probes (SEQ ID NOs. 2024-2025) can also be used to detect the high-level penicillin resistance 383-bp amplicon. Five internal probes containing all possible mutations to detect the 157-bp amplicon which includes intermediate- and high-level penicillin resistance were also designed (SEQ ID NOs. 1094, 1192-1193, 1214 and 1216). Design and synthesis of primers and probes, and detection of the probe hybridization were performed as described in Example 7. Annex XXXI illustrates one of the internal probe for detection of the high-level penicillin resistance 383-bp amplicon (SEQ ID NO. 1197) and one of the internal probe for detection of the intermediate- and high-level penicillin resistance 157-bp amplicon (SEQ ID NO. 1193).

PCR amplification. For all bacterial species, amplification was performed from purified genomic DNA using a PTC-200 thermocycler (MJ Research). 1 μl of genomic DNA at 0.1 ng/μl, or 1 μl of a bacterial lysate, was transferred to a 19 μl PCR mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (H 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 0.1 μM (each) of the S. pneumoniae-specific primers SEQ ID NO. 1179 and SEQ ID NO. 1181, 0.2 μM of primer SEQ ID NO. 1129, 0.7 μM of primer SEQ ID NO. 1131, and 0.6 μM of primer SEQ ID NO. 1130, 0.05 mM bovine serum albumin (BSA), and 0.5 U Taq polymerase (Promega) coupled with TaqStart™ antibody. In order to generate Digoxigenin (DIG)-labeled amplicons for capture probe hybridization, 0.1×PCR DIG labeling four deoxynucleoside triphosphates mix (Boehringer Mannheim GmbH) was used for amplification.

For determination of the sensitivity of the PCR assays, 10-fold dilutions of purified genomic DNA were used to determine the minimal number of genome copies which can be detected.

Capture probe hybridization. The DIG-labeled amplicons were hybridized to the capture probes bound to 96-well plates. The plates were incubated with anti-DIG-alkaline phosphatase and the chemiluminescence was measured by using a luminometer (MLX, Dynex Technologies Inc.) after incubation with CSPD and recorded as Relative Light Unit (RLU). The RLU ratio of tested sample with and without captures probes was then calculated. A ratio 2.0 was defined as a positive hybridization signal. All reactions were performed in duplicate.

Results

Amplifications with the multiplex PCR assay. The specificity of the assay was assessed by performing 40-cycle PCR amplifications with the panel of gram-positive (67 species from 12 genera) and gram-negative (33 species from 17 genera) bacterial species listed in Table 13. All bacterial species tested other than S. pneumoniae were negative except S. mitis and S. oralis. Ubiquity tests were performed using a collection of 98 S. pneumoniae strains including high-level penicillin resistance (n=53), intermediate resistance (n=12) and sensitive (n=33) strains. There was a perfect correlation between PCR and standard susceptibility testing for 33 penicillin-sensitive isolates. Among 12 S. pneumoniae isolates with intermediate penicillin resistance based on susceptibility testing, 11 had intermediate resistance based on PCR, but one S. pneumoniae isolate with penicillin MIC of 0.25 μg/ml showed a high-level penicillin resistance based on genotyping. Among 53 isolates with high-level penicillin resistance based on susceptibility testing, 51 had high-level penicillin resistance based on PCR but two isolates with penicillin MIC>1 μg/ml showed an intermediate penicillin resistance based on genotyping. In general, there was a good correlation between the genotype and classical culture method for bacterial identification and susceptibility testing.

The sensitivity of the S. pneumoniae-specific assay with 40-cycle PCR protocols was determined by using purified genomic DNA from 9 isolates of S. pneumoniae. The detection limit was around 10 copies of genomic DNA for all of them.

Post-PCR hybridization with internal probes. The specificity of the multiplex PCR assay coupled with capture-probe hybridization was tested with 98 strains of S. pneumoniae, 16 strains of S. mitis and 3 strains of S. oralis. The internal probe specific to S. pneumoniae (SEQ ID NO. 1180) detected all 98 S. pneumoniae strains but did not hybridize to the S. mitis and S. oralis amplicons. The five internal probes specific to the high-level resistance amplicon (SEQ ID NOs. 1197, 1217-1220) detected all amplification patterns corresponding to high-level resistance. The two S. pneumoniae strains with penicillin MIC>1 μg/ml that showed an intermediate penicillin resistance based on PCR amplification were also intermediate resistance based on probe hybridization. Similarly, among 12 strains with intermediate-penicillin resistance based on susceptibility testing, 11 showed intermediate-penicillin resistance based on hybridization with the five internal probes specific to the intermediate and high-level resistance amplicon (SEQ ID NOs. 1094, 1192-1193, 1214 and 1216). The strain described above having a penicillin MIC of 0.25 μg/ml which was high-level penicillin resistance based on PCR amplification was also high-level resistance based on probe hybridization. In summary, the combination of the multiplex PCR and hybridization assays results in a highly specific test for the detection of penicillin-resistant Streptococcus pneumoniae.

Assay II:

Bacterial strains. The specificity of the multiplex PCR assay was verified by using the same strains as those used for the development of Assay I. The penicillin MICs (minimal inhibitory concentrations) were measured by the broth dilution method according to the recommended protocol of NCCLS.

PCR primers and internal probes. The analysis of pbp1a sequences from S. pneumoniae strains with various levels of penicillin resistance from public databases and from the database described in Example 18 allowed the design of two primers located in the constant region of pbp1a. PCR primer pair (SEQ ID NOs. 2015 and 2016) was designed to amplify a 888-bp variable region of pbp1a from all S. pneumoniae strains. A series of internal probes were designed for identification of the pbp1a mutations associated with penicillin resistance in S. pneumoniae. For detection of high-level penicillin resistance (MICs≧1 μg/ml), three internal probes were designed (SEQ ID NOs. 2017-2019). Alternatively, ten other internal probes were designed that can also be used for detection of high-level resistance within the 888-bp pbp1a amplicon: (1) three internal probes for identification of the amino acid substitutions Thr-371 to Ser or Ala within the motif S370TMK (SEQ ID NOs. 2031-2033); (2) two internal probes for detection of the amino acid substitutions Ile-459 to Met and Ser-462 to Ala near the motif S428RN (SEQ ID NOs. 1135 and 2026); (3) two internal probes for identification of the amino acid substitutions Asn-443 to Asp (SEQ ID NOs. 1134 and 2027); and (4) three internal probes for detection of all sequence variations within another region (SEQ ID NOs. 2028-2030). For detection of high-level and intermediate penicillin resistance (MICs 0.25 μg/ml), four internal probes were designed (SEQ ID NOs. 2020-2023). Alternatively, six other internal probes were designed for detection of the four consecutive amino acid substitutions T574SQF to A574TGY near the motif K557TG (SEQ ID NOs. 2034-2039) that can also be used for detection of intermediate- and high-level resistance within the 888-bp pbp1a amplicon.

PCR amplification. For all bacterial species, amplification was performed from purified genomic DNA using a PTC-200 thermocycler (MJ Research). 1 μl of genomic DNA at 0.1 ng/μl, or 1 μl of a bacterial lysate, was transferred to a 19 μl PCR mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 0.08 μM (each) of the S. pneumoniae-specific primers SEQ ID NO. 1179 and SEQ ID NO. 1181, 0.4 μM of the pbp1a-specific primer SEQ ID NO. 2015, 1.2 μM of pbp1a-specific primer SEQ ID NO. 2016, 0.05 mM bovine serum albumin (BSA), and 0.5 U Taq polymerase (Promega) coupled with TaqStart™ antibody. In order to generate Digoxigenin (DIG)-labeled amplicons for capture probe hybridization, 0.1×PCR DIG labeling four deoxynucleoside triphosphates mix (Boehringer Mannheim GmbH) was used for amplification.

For determination of the sensitivities of the PCR assays, 10-fold dilutions of purified genomic DNA were used to determine the minimal number of genome copies which can be detected.

Capture probe hybridization. The DIG-labeled amplicons were hybridized to the capture probes bound to 96-well plates as described for Assay I.

Results

Amplifications with the multiplex PCR assay. The specificity of the assay was assessed by performing 40-cycle PCR amplifications with the panel of gram-positive (67 species from 12 genera) and gram-negative (33 species from 17 genera) bacterial species listed in Table 13. All bacterial species tested other than S. pneumoniae were negative except S. mitis and S. oralis. Ubiquity tests were performed using a collection of 98 S. pneumoniae strains including high-level penicillin resistance (n=53), intermediate resistance (n=12) and sensitive (n=33) strains. All the above S. pneumoniae strains produced the 888-bp amplicon corresponding to pbp1a and the 241-bp fragment corresponding to hexA.

The sensitivity of the S. pneumoniae-specific assay with 40-cycle PCR protocols was determined by using purified genomic DNA from 9 isolates of S. pneumoniae. The detection limit was around 10 copies of genomic DNA for all of them.

Post-PCR hybridization with internal probes. The specificity of the multiplex PCR assay coupled with capture-probe hybridization was tested with 98 strains of S. pneumoniae, 16 strains of S. mitis and 3 strains of S. oralis. The internal probe specific to S. pneumoniae (SEQ ID NO. 1180) detected all 98 S. pneumoniae strains but did not hybridize to the S. mills and S. oralis amplicons. The three internal probes (SEQ ID NOs 2017-2019) specific to high-level resistance detected all the 43 strains with high-level penicillin resistance based on susceptibility testing. Among 12 isolates with intermediate-penicillin resistance based on susceptibility testing, 11 showed intermediate-penicillin resistance based on hybridization with 4 internal probes (SEQ ID NOs. 2020-2023) and one strain having penicillin MIC of 0.25 μg/ml was misclassified as high-level penicillin resistance. In summary, the combination of the multiplex PCR and hybridization assays results in a highly specific test for the detection of penicillin-resistant Streptococcus pneumoniae.

Example 21 Sequencing of the Vancomycin Resistance vanA, vanC1, vanC2 and vanC3 Genes

The publicly available sequences of the vanH-vanA-vanX-vanY locus of transposon Tnl546 from E. faecalis, vanC1 sequence from one strain of E. gallinarum, vanC2 and vanC3 sequences from a variety of E. casseliflavus and E. flavescens strains, respectively, allowed the design of PCR primers able to amplify the vanA, vanC1, vanC2 and vanC3 sequences of several Enterococcus species. Using primer pairs van6877 and van9106 (SEQ ID NOs. 1150 and 1155), vanC1-122 and vanC1-1315 (SEQ ID NOs. 1110 and 1109), and vanC2C3-1 and vanC2C3-1064 (SEQ ID NOs. 1108 and 1107), it was possible to amplify and determine vanA sequences SEQ ID NOs. 1049-1057, vanC1 sequences SEQ ID NOs. 1058-1059, vanC2 sequences SEQ ID NOs. 1060-1063 and vanC3 sequences SEQ ID NOs. 1064-1066, respectively. Four other PCR primers (SEQ ID NOs. 1151-1154) were also designed and used to complete the sequencing of vanA amplification products.

Example 22 Development of a PCR Assay for the Detection and Identification of Enterococci at Genus and Species Levels and its Associated Resistance Genes vanA and vanB

The comparison of vanA and vanB sequences revealed conserved regions allowing the design of PCR primers specific to both vanA and vanB sequences (Annex XXXVIII). The PCR primer pair vanAB459 and vanAB830R (SEQ ID NOs. 1112 and 1111) was used in multiplex with the Enterococcus-specific primers Encg313dF and Encg599c (SEQ ID NOs. 1137 and 1136) described in Example 11. Sequence alignment analysis of vanA and vanB sequences revealed regions suitable for the design of internal probes specific to vanA (SEQ ID NO. 1170) and vanB (SEQ ID NO. 1171). PCR amplification and agarose gel electrophoresis of the amplified products were performed as described in Example 11. The optimal cycling conditions for maximum sensitivity and specificity were found to be 3 min. at 94° C., followed by forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 62° C., plus a terminal extension at 72° C. for 2 minutes. The specificity of the multiplex assay with 40-cycle PCR was verified by using 0.1 nanogram of purified genomic DNA from a panel of bacteria listed in Table 10. The sensitivity of the multiplex assay with 40-cycle PCR was verified with three strains of E. casseliflavus, eight strains of E. gallinarum, two strains of E. flavescens, two vancomycin-resistant strains of E. faecalis and one vancomycin-sensitive strain of E. faecalis, three vancomycin-resistant strains of E. faecium, one vancomycin-sensitive strain of E. faecium and one strain of each of the other enterococcal species listed in Table 10. The detection limit was 1 to 10 copies of genomic DNA, depending on the enterococcal species tested. The vanA- and vanB-specific internal probes (SEQ ID NOs. 1170 and 1171), as well as the E. faecalis- and E. faecium-specific internal probes (SEQ ID NOs. 1174 and 602) and the internal probe specific to the group including E. casseliflavus, E. gallinarum and E. flavescens (SEQ ID NO. 1122) described in Example 11, were able to recognize vancomycin-resistant enterococcal species with high sensitivity, specificity and ubiquity showing a perfect correlation between the genotypic and phenotypic analysis.

The format of the assay is not limited to the one described above. A person skilled in the art could adapt the assay for different formats such as PCR with real-time detection using molecular beacon probes. Molecular beacon probes designed to be used in this assay include, but are not limited to, SEQ ID NO. 1236 for the detection of E. faecalis, SEQ ID NO. 1235 for the detection of E. faecium, SEQ ID NO. 1240 for the detection of vanA, and SEQ ID NO. 1241 for the detection of vanB.

Example 23 Development of a Multiplex PCR Assay for Detection and Identification of Vancomycin-Resistant Organisms Including Enterococcus faecalis, Enterococcus faecium and the Group Including Enterococcus gallinarum, Enterococcus Casseliflavus, and Enterococcus flavescens.

The vanA and vanB genes encode the major glycopeptide resistance phenotypes in vancomycin resistant microorganisms. To design an assay to detect vancomycin resistant microorganisms, the nucleotide sequence of the vanA and vanB genes were analyzed. FIGS. 13 and 14 show a nucleotide sequence alignment of the vanA and vanB genes from the bacterial strains listed in Tables 26 and 27, respectively. Shown above the sequence alignments is a consensus DNA sequence derived from the multiple sequences. The analysis of vanA and vanB sequences revealed conserved regions allowing design of PCR primer pairs (SEQ ID NOs. 1089 and 1090 and SEQ ID NOs: 1090 and 1091) specific to vanA sequences (Annex XXVIII) and PCR primer pairs (SEQ ID NOs. 1095 and 1096 and SEQ ID NOs: 2298 and 1096) specific to vanB sequences (Annex XXIX). Shown below the sequence alignments in FIGS. 13 and 14 is the sequence and location of the vanA primers SEQ ID NO: 1090 and 1091 and the vanB primers SEQ ID NOs: 2298 and 1096, respectively. Also shown are the sequence and location of molecular beacon probes, SEQ ID NOs: 2299, 2300, designed for the detection of the vanA and vanB amplification products, respectively. SEQ ID NO: 2299. The vanA molecular beacon (SEQ ID NO: 2299) contains a 5′ carboxyfluorescein (FAM) fluorophore. The vanB molecular beacon (SEQ ID NO: 2300) contains a sulforhodamine active ester (Texas Red) at its 5′ end. Both beacons contain the nonfluorescent quencher moiety dabcyl chloride (DABCYL) at their 3′ ends.

An internal control DNA, pERVd (SEQ ID NO: 2302) was designed for the vanR assay. The primers of SEQ ID NO: 1090 and SEQ ID NO: 1096 can hybridize to produce and amplification product from the internal control DNA. A molecular beacon probe (SEQ ID NO: 2301) was designed to detect the amplification product of the internal control DNA. SEQ ID NO: 2301 contains a 5′ tetrachlorofluorescein (TET) fluorophore and the DABCYL quencher moiety at its 3′ end.

In a first experiment, the vanA-specific PCR primer pair (SEQ ID. NOs. 1089 and 1090) was used in multiplex with the vanB-specific PCR primer pair described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NOs. 1095 and 1096 in the present patent and SEQ ID NOs. 231 and 232 in the said patent). The comparison of vanC1, vanC2 and vanC3 sequences revealed conserved regions allowing design of PCR primers (SEQ ID NOs. 1101 and 1102) able to generate a 158-bp amplicon specific to the group including E. gallinarum, E. casseliflavus and E. flavescens (Annex XXX). The vanC-specific PCR primer pair (SEQ ID NOs. 1101 and 1102) was used in multiplex with the E. faecalis-specific PCR primer pair described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NOs. 40 and 41 in the said patent) and with the E. faecium-specific PCR primer pair described in our patent publication WO98/20157 (SEQ ID NOs. 1 and 2 in the said publication). For both multiplexes, the optimal cycling conditions for maximum sensitivity and specificity were found to be 3 min. at 94° C., followed by forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 58° C., plus a terminal extension at 72° C. for 2 minutes. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide. The vanA-specific PCR primer pair (SEQ ID NOs. 1089 and 1090), the vanB-specific primer pair (SEQ ID NOs. 1095 and 1096) and the vanC-specific primer pair (SEQ ID NOs. 1101 and 1102) were tested for their specificity by using 0.1 nanogram of purified genomic DNA from a panel of 5 vancomycin-sensitive Enterococcus species, 3 vancomycin-resistant Enterococcus species, 13 other gram-positive bacteria and one gram-negative bacterium. Specificity tests were performed with the E. faecium-specific PCR primer pair described in our patent publication WO98/20157 (SEQ ID NOs. 1 and 2 in the said publication) and with the E. faecalis-specific PCR primer pair described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NOs. 40 and 41 in the said patent) on a panel of 37 gram-positive bacterial species. All Enterococcus strains were amplified with high specificity showing a perfect correlation between the genotypic and phenotypic analysis. The sensitivity of the assays was determined for several strains of E. gallinarum, E. casseliflavus, E. flavescens and vancomycin-resistant E. faecalis and E. faecium. Using each of the E. faecalis- and E. faecium-specific PCR primer pairs as well as vanA-, vanB- and vanC-specific PCR primers used alone or in multiplex as described above, the sensitivity ranged from 1 to 10 copies of genomic DNA.

The format of the assay is not limited to the one described above. A person skilled in the art could adapt the assay for different formats such as PCR with real-time detection using molecular beacon probes. Molecular beacon probes designed to be used in this assay include, but are not limited to, SEQ ID NO. 1238 for the detection of E. faecalis, SEQ ID NO. 1237 for the detection of E. faecium, SEQ ID NO. 1239 for the detection of vanA, and SEQ ID NO. 1241 for the detection of vanB.

Another PCR assay was developed for the detection of vancomycin-resistant E. faecium and vancomycin-resistant E. faecalis. This assay included two multiplex: (1) the first multiplex contained the vanA-specific primer pair (SEQ ID NOs. 1090-1091) and the vanB-specific PCR primer pair described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NOs. 1095 and 1096 in the present patent and SEQ ID NOs. 231 and 232 in the said patent), and (2) the second multiplex contained the E. faecalis-specific PCR primer pair described in our assigned U.S. Pat. No. 5,994,066 (SEQ ID NOs. 40 and 41 in the said patent) and the E. faecium-specific PCR primer pair described in our patent publication WO98/20157 (SEQ ID NOs. 1 and 2 in the said publication). For both multiplexes, the optimal cycling conditions for maximum sensitivity and specificity were found to be 3 min. at 94° C., followed by forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 58° C., plus a terminal extension at 72° C. for 2 minutes. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide. The two multiplexes were tested for their specificity by using 0.1 nanogram of purified genomic DNA from a panel of two vancomycin-sensitive E. faecalis strains, two vancomycin-resistant E. faecalis strains, two vancomycin-sensitive E. faecium strains, two vancomycin-resistant E. faecium strains, 16 other enterococcal species and 31 other gram-positive bacterial species. All the E. faecium and E. faecalis strains were amplified with high specificity showing a perfect correlation between the genotypic analysis and the susceptibility to glycopeptide antibiotics (vancomycin and teicoplanin). The sensitivity of the assay was determined for two vancomycin-resistant E. faecalis strains and two vancomycin-resistant E. faecium strains. The detection limit was 5 copies of genomic DNA for all the strains.

This multiplex PCR assay was coupled with capture-probe hybridization. Four internal probes were designed: one specific to the vanA amplicon (SEQ ID NO. 2292), one specific to the vanB amplicon (SEQ ID NO. 2294), one specific to the E. faecalis amplicon (SEQ ID NO. 2291) and one specific to the E. faecium amplicon (SEQ ID NO. 2287). Each of the internal probes detected their specific amplicons with high specificity and sensitivity.

The VanR Assay Development

In a next set of experiments, a multiplex real-time PCR reaction (the VanR assay) using the vanA primer pair SEQ ID NO: 1090 and 1091, the vanB primer pair SEQ ID NO: 1096 and 2298, the internal control DNA SEQ ID NO: 2302, and the molecular beacon probes SEQ ID NOs: 2299, 2300, and 2301 was performed.

For the template DNA, purified genomic DNA from vanA resistant Enterococcus faecium or vanB resistant Enterococcus faecalis was obtained from strains grown on blood agar plates under standard conditions. Genomic DNA was extracted from the cultures using the GNOME kit (QBIOgene, Carlsbad, Calif.) according to the manufacturer's instructions. Template DNA samples were treated with RNase prior to quantitation. Genomic DNA concentration was determined and the quality of the genomic DNA preparations was confirmed using conventional methods.

Lyophilized reagents listed in Table 24 were used for the VanR assay. The lyophilized reagents were reconstituted with 225 μl diluent (116 mM Tris-HCl, pH 8.3, 11.6 mM KCl, 3.48 mM MgCl₂, 5.8 mM NH₂SO₄) and subsequently divided into 25 μl aliquots. 0.5, 2.5, 5, 10 or 20 copies of template DNA was added to each of 5 replicate reactions.

The VanR assay PCR was run in a SMART CYCLER™ PCR machine under the following conditions: 60° C. for 6 sec, followed by 95° C. for 900 sec, followed by 45 cycles of 95° C. for 5 seconds, 63° C. for 10 sec and 72° C. for 20 sec. The fluorescent readout from the FAM channel (vanA) and the Texas Red channel (vanB) of the reactions is shown in FIGS. 13A and 13B, respectively. The VanR assay is capable of detecting 5 copies of vanA target DNA in a sample (FIG. 13A) and of detecting 10 copies of vanB target DNA in a sample (FIG. 13B). For each concentration of template DNA, the number of positive assay results out of each of the five replicates was recorded (Table 15).

Specificity

To demonstrate the specificity of the VanR assay, vanC, vanD, vanE, and vanG resistant enterococci, other closely related bacteria, normal and pathogenic anal or fecal flora, or human DNA as listed in Tables 16-18 were assayed as follows: VanR assay lyophilized reagents (Table 38) were reconstituted with 225 μl diluent and aliquoted as described above. Template DNA was prepared using conventional methods and diluted in sample preparation buffer to a final concentration of 0.33 ng/μl. 3 μl template DNA was added to each master mix, and the reaction was carried out as described above in the SMART CYCLER™ PCR machine. 41 electrophoresis loading buffer was added to the reactions upon completion, and 15 μl of each reaction was run on an agarose gel to view the PCR amplification products, as shown in FIGS. 14-17.

To assess the specificity of the molecular beacons in the VanR assay, PCR assays were preformed to test cross-reactivity with amplified vanA and vanB target DNA and internal control DNA. The reaction components listed in Table 34 were each added to premix in Table 33. For each reaction, 25.8 μl of the final mix was combined with 3 μl template DNA (either 25 copies vanA DNA or 50 copies vanB DNA) or TE buffer (1×), as indicated. The reactions were performed in the SMART CYCLER™ PCR machine using the VanR assay conditions as described above. Table 35 shows the results of the experiment. Positive results were obtained in the FAM channel in every reaction that contained vanA template DNA and the vanA primers. Positive results were obtained in the Texas Red channel in every reaction that contained vanB template DNA and vanB primers. Positive results obtained in the TET channel in every reaction that contained internal control template DNA and internal control primers.

Negative results were obtained in each channel for every reaction that did not contain a target DNA that could be amplified and detected using the indicated molecular beacon probe. In other words, the molecular beacon probes did not cross-react with non-specific DNAs. FIGS. 18A-20B show the fluorescent readouts of the experiments.

Validation with Clinical Samples

To validate the VanR assay, the sensitivity of the VanR assay was performed on clinical samples. Briefly, the VanR assay lyophilized reagents listed in Table 38 were reconstituted in 225 μl diluent and aliquoted as described above. DNA isolation and quantitation was performed using conventional techniques. The samples were processed in a SMART CYCLER' PCR machine using the VanR reaction conditions described above.

FIG. 21 shows the fluorescent readout in the FAM (vanA) channel and the Texas Red channel (vanB) from a specimen that is vanA resistant. The reaction gave a positive result in the FAM channel but not the Texas Red channel. FIG. 22 shows the fluorescent readout in the FAM and Texas Red channels from a combination of a vanA resistant specimen and a vanB resistant specimen. Positive results were obtained in both the FAM and the Texas Red channel. FIG. 23 shows the fluorescent readout in the FAM and Texas Red channels from a vanB positive specimen. The results were negative in the FAM channel, and positive in the Texas Red channel.

Sensitivity

To assess the sensitivity of the VanR assay, template DNA isolated from enterococci from various geographic regions, and on template DNA from vanB resistant bacterial species other than enterococci was isolated and tested in the VanR assay as described above. Table 36 lists the enterococcal strains from various regions in the world tested in the assay. The table identifies the vanA and vanB phenotype of each strain. PCR amplification products were detected by running a sample of each reaction on an agarose gel, shown in FIG. 24. vanA or vanB PCR amplification products were detectable in each of the strains tested. Table 37 lists non-enterococcal, vanB resistant strains tested in the VanR assay. The PCR amplification products are shown in FIG. 25. The reaction produced an amplification product of the expected size for the vanB amplicon.

These results demonstrate that the VanR assay is sensitive and specific.

Example 24 Universal Amplification Involving the EF-G (fusA) Subdivision of tuf Sequences

As shown in FIG. 3, primers SEQ ID NOs. 1228 and 1229 were designed to amplify the region between the end of fusA and the beginning of tuf genes in the str operon. Genomic DNAs from a panel of 35 strains were tested for PCR amplification with those primers. In the initial experiment, the following strains showed a positive result: Abiotrophia adiacens ATCC 49175, Abiotrophia defectiva ATCC 49176, Bacillus subtilis ATCC 27370, Clostridium difficile ATCC 9689, Enterococcus avium ATCC 14025, Enterococcus casseliflavus ATCC 25788, Enterococcus cecorum ATCC 43198, Enterococcus faecalis ATCC 29212, Enterococcus faecium ATCC 19434, Enterococcus flavescens ATCC 49996, Enterococcus gallinarum ATCC 49573, Enterococcus solitarius ATCC 49428, Escherichia coli ATCC 11775, Haemophilus influenzae ATCC 9006, Lactobacillus acidophilus ATCC 4356, Peptococcus niger ATCC 27731, Proteus mirabilis ATCC 25933, Staphylococcus aureus ATCC 43300, Staphylococcus auricularis ATCC 33753, Staphylococcus capitis ATCC 27840, Staphylococcus epidemidis ATCC 14990, Staphylococcus haemolyticus ATCC 29970, Staphylococcus hominis ATCC 27844, Staphylococcus lugdunensis ATCC 43809, Staphylococcus saprophyticus ATCC 15305, Staphylococcus simulans ATCC 27848, and Staphylococcus warneri ATCC 27836. This primer pair could amplify additional bacterial species; however, there was no amplification for some species, suggesting that the PCR cycling conditions could be optimized or the primers modified. For example, SEQ ID NO. 1227 was designed to amplify a broader range of species.

In addition to other possible primer combinations to amplify the region covering fusA and tuf, FIG. 3 illustrates the positions of amplification primers SEQ ID NOs. 1221-1227 which could be used for universal amplification of fusA segments. All of the above mentioned primers (SEQ ID NOs. 1221-1229) could be useful for the universal and/or the specific detection of bacteria.

Moreover, different combinations of primers SEQ ID NOs. 1221-1229, sometimes in combination with tuf sequencing primer SEQ ID NO. 697, were used to sequence portions of the str operon, including the intergenic region. In this manner, the following sequences were generated: SEQ ID NOs. 1518-1526, 1578-1580, 1786-1821, 1822-1834, 1838-1843, 2184, 2187, 2188, 2214-2249, and 2255-2269.

Example 25 DNA Fragment Isolation from Staphylococcus saprophyticus by Arbitrarily Primed PCR

DNA sequences of unknown coding potential for the species-specific detection and identification of Staphylococcus saprophyticus were obtained by the method of arbitrarily primed PCR (AP-PCR).

AP-PCR is a method which can be used to generate specific DNA probes for microorganisms (Fani et al., 1993, Molecular Ecology 2:243-250). A description of the AP-PCR protocol used to isolate a species-specific genomic DNA fragment from Staphylococcus saprophyticus follows. Twenty different oligonucleotide primers of 10 nucleotides in length (all included in the AP-PCR kit OPAD (Operon Technologies, Inc., Alameda, Calif.)) were tested systematically with DNAs from 5 bacterial strains of Staphylococcus saprophyticus as well as with bacterial strains of 27 other staphylococcal (non-S. saprophyticus) species. For all bacterial species, amplification was performed directly from one μL (0.1 ng/μL) of purified genomic DNA. The 25 μL PCR reaction mixture contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 1.2 μM of only one of the 20 different AP-PCR primers OPAD, 200 μM of each of the four dNTPs, 0.5 U of Taq DNA polymerase (Promega Corp., Madison, Wis.) coupled with TaqStart™ antibody (Clontech Laboratories Inc., Palo Alto, Calif.). PCR reactions were subjected to cycling using a MJ Research PTC-200 thermal cycler as follows: 3 min at 96° C. followed by 42 cycles of 1 min at 94° C. for the denaturation step, 1 min at 31° C. for the annealing step and 2 min at 72° C. for the extension step. A final extension step of 7 min at 72° C. followed the 42 cycles to ensure complete extension of PCR products. Subsequently, twenty microliters of the PCR-amplified mixture were resolved by electrophoresis on a 1.5% agarose gel containing 0.25 μg/ml of ethidium bromide. The size of the amplification products was estimated by comparison with a 50-bp molecular weight ladder.

Amplification patterns specific for Staphylococcus saprophyticus were observed with the AP-PCR primer OPAD-16 (sequence: 5′-AACGGGCGTC-3′). Amplification with this primer consistently showed a band corresponding to a DNA fragment of approximately 380 by for all Staphylococcus saprophyticus strains tested but not for any of the other staphylococcal species tested.

The band corresponding to the 380 by amplicon, specific and ubiquitous for S. saprophyticus based on AP-PCR, was excised from the agarose gel and purified using the QIAquick™ gel extraction kit (QIAGEN Inc.). The gel-purified DNA fragment was cloned into the T/A cloning site of the pCR 2.1™ plasmid vector (Invitrogen Inc.) using T4 DNA ligase (New England BioLabs). Recombinant plasmids were transformed into E. coli DH5α competent cells using standard procedures. All reactions were performed according to the manufacturer's instructions. Plasmid DNA isolation was done by the method of Birnboim and Doly (Nucleic Acid Res., 1979, 7:1513-1523) for small-scale preparations. All plasmid DNA preparations were digested with the EcoRI restriction endonuclease to ensure the presence of the approximately 380 by AP-PCR insert into the plasmid. Subsequently, a large-scale and highly purified plasmid DNA preparation was performed from two selected clones shown to carry the AP-PCR insert by using the QIAGEN plasmid purification kit (midi format). These large-scale plasmid preparations were used for automated DNA sequencing.

The 380 by nucleotide sequence was determined for three strains of S. saprophyticus (SEQ ID NOs. 74, 1093, and 1198). Both strands of the AP-PCR insert from the two selected clones were sequenced by the dideoxynucleotide chain termination sequencing method with SP6 and T7 sequencing primers by using the Applied Biosystems automated DNA sequencer (model 373A) with their PRISM™ Sequenase® Terminator Double-stranded DNA Sequencing Kit (Applied Biosystems, Foster City, Calif.).

Optimal species-specific amplification primers (SEQ ID NOs. 1208 and 1209) have been selected from the sequenced AP-PCR Staphylococcus saprophyticus DNA fragments with the help of the primer analysis software Oligo™ 5.0 (National BioSciences Inc). The selected primers were tested in PCR assays to verify their specificity and ubiquity. Data obtained with DNA preparations from reference ATCC strains of 49 gram-positive and 31 gram-negative bacterial species, including 28 different staphylococcal species, indicate that the selected primer pairs are specific for Staphylococcus saprophyticus since no amplification signal has been observed with DNAs from the other staphylococcal or bacterial species tested. This assay was able to amplify efficiently DNA from all 60 strains of S. saprophyticus from various origins tested. The sensitivity level achieved for three S. saprophyticus reference ATCC strains was around 6 genome copies.

Example 26 Sequencing of Prokaryotic tuf Gene Fragments

The comparison of publicly available tuf sequences from a variety of bacterial species revealed conserved regions, allowing the design of PCR primers able to amplify tuf sequences from a wide range of bacterial species. Using primer pair SEQ ID NOs. 664 and 697, it was possible to amplify and determine tuf sequences SEQ ID NOs.: 1-73, 75-241, 607-618, 621, 662, 675, 717-736, 868-888, 932, 967-989, 992, 1002, 1572-1575, 1662-1663, 1715-1733, 1835-1837, 1877-1878, 1880-1881, 2183, 2185, 2200, 2201, and 2270-2272.

Example 27 Sequencing of Procaryotic recA Gene Fragments

The comparison of publicly available recA sequences from a variety of bacterial species revealed conserved regions, allowing the design of PCR primers able to amplify recA sequences from a wide range of bacterial species. Using primer pairs SEQ ID NOs. 921-922 and 1605-1606, it was possible to amplify and determine recA sequences SEQ ID NOs.: 990-991, 1003, 1288-1289, 1714, 1756-1763, 1866-1873 and 2202-2212.

Example 28 Specific Detection and Identification of Escherichia coli/Shigella Sp. Using tuf Sequences

The analysis of tuf sequences from a variety of bacterial species allowed the selection of PCR primers (SEQ ID NOs. 1661 and 1665) and of an internal probe (SEQ ID NO. 2168) specific to Escherichia coli/Shigella sp. The strategy used to design the PCR primers was based on the analysis of a multiple sequence alignment of various tuf sequences. The multiple sequence alignment included the tuf sequences of Escherichia coli/Shigella sp. as well as tuf sequences from other species and bacterial genera, especially representatives of closely related species. A careful analysis of this alignment allowed the selection of oligonucleotide sequences which are conserved within the target species but which discriminate sequences from other species, especially from the closely related species, thereby permitting the species-specific and ubiquitous detection and identification of the target bacterial species.

The chosen primer pair, oligos SEQ ID NOs. 1661 and 1665, gives an amplification product of 219 bp. Standard PCR was carried out using 0.4 μM of each primer, 2.5 mM MgCl₂, BSA 0.05 mM, 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, dNTPs 0.2 mM (Pharmacia), 0.5 U Taq DNA polymerase (Promega) coupled with TaqStart™ antibody (Clontech Laboratories Inc.), 1 μl of genomic DNA sample in a final volume of 20 μl using a PTC-200 thermocycler (MJ Research). The optimal cycling conditions for maximum sensitivity and specificity were 3 minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 60° C., followed by terminal extension at 72° C. for 2 minutes. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide. Visualization of the PCR products was made under UV at 254 nm.

Specificity of the assay was tested by adding to the PCR reactions 0.1 ng of genomic DNA from each of the following bacterial species: Escherichia coli (7 strains), Shigella sonnei, Shigella flexneri, Shigella dysenteriae, Salmonella typhimyurium, Salmonella typhi, Salmonella enteritidis, Tatumella ptyseos, Klebsiella pneumoniae (2 strains), Enterobacter aerogenes, Citrobacter farmeri, Campylobacter jejuni, Serratia marcescens. Amplification was observed only for the Escherichia coli and Shigella sp. strains listed and Escherichia fergusonii. The sensitivity of the assay with 40-cycle PCR was verified with one strain of E. coli and three strains of Shigella sp. The detection limit for E. coli and Shigella sp. was 1 to 10 copies of genomic DNA, depending on the strains tested.

Example 29 Specific Detection and Identification of Klebsiella pneumoniae Using atpD Sequences

The analysis of atpD sequences from a variety of bacterial species allowed the selection of PCR primers specific to K. pneumoniae. The primer design strategy is similar to the strategy described in Example 28 except that atpD sequences were used in the alignment.

Two K. pneumoniae-specific primers were selected, (SEQ ID NOs. 1331 and 1332) which give an amplification product of 115 bp. Standard PCR was carried out on PTC-200 thermocyclers (MJ Research) using 0.4 μM of each primer as described in Example 28. The optimal cycling conditions for maximum sensitivity and specificity were as follow: three minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 55° C., followed by terminal extension at 72° C. for 2 minutes.

Specificity of the assay was tested by adding to the PCR reactions 0.1 ng of genomic DNA from each of the following bacterial species: Klebsiella pneumoniae (2 strains), Klebsiella ornitholytica, Klebsiella oxytoca (2 strains), Klebsiella planticola, Klebsiella terrigena, Citrobacter freundii, Escherichia coli, Salmonella cholerasuis typhi, Serratia marcescens, Enterobacter aerogenes, Proteus vulgaris, Kluyvera ascorbata, Kluyvera georgiana, Kluyvera cryocrescens and Yersinia enterolitica. Amplification was detected for the two K. pneumoniae strains, K. planticola, K. terrigena and the three Kluyvera species tested. Analysis of the multiple alignment sequence of the atpD gene allowed the design of an internal probe SEQ ID NO. 2167 which can discriminate Klebsiella pneumoniae from other Klebsiella sp. and Kluyvera sp. The sensitivity of the assay with 40-cycle PCR was verified with one strain of K. pneumoniae. The detection limit for K. pneumoniae was around 10 copies of genomic DNA.

Example 30 Specific Detection and Identification of Acinetobacter baumannii Using atpD Sequences

The analysis of atpD sequences from a variety of bacterial species allowed the selection of PCR primers specific to Acinetobacter baumannii. The primer design strategy is similar to the strategy described in Example 28.

Two A. baumannii-specific primers were selected, SEQ ID NOs. 1690 and 1691, which give an amplification product of 233 bp. Standard PCR was carried out on PTC-200 thermocyclers (MJ Research) using 0.4 μM of each primer as described in Example 28. The optimal cycling conditions for maximum sensitivity and specificity were as follow: three minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 60° C., followed by terminal extension at 72° C. for 2 minutes.

Specificity of the assay was tested by adding to the PCR reactions 0.1 ng of genomic DNA from each of the following bacterial species: Acinetobacter baumannii (3 strains), Acinetobacter anitratus, Acinetobacter lwoffi, Serratia marcescens, Enterobacter cloacae, Enterococcus faecalis, Pseudomonas aeruginosa, Psychrobacter phenylpyruvicus, Neisseria gonorrheoae, Haemophilus haemoliticus, Yersinia enterolitica, Proteus vulgaris, Eikenella corrodens, Escherichia coli. Amplification was detected only for A. baumannii, A. anitratus and A. lwoffi. The sensitivity of the assay with 40-cycle PCR was verified with two strains of A. baumannii. The detection limit for the two A. baumannii strains tested was 5 copies of genomic DNA. Analysis of the multiple alignment sequence of the atpD gene allowed the design of a A. baumannii-specific internal probe (SEQ ID NO. 2169).

Example 31 Specific Detection and Identification of Neisseria gonorrhoeae Using tuf Sequences

The analysis of tuf sequences from a variety of bacterial species allowed the selection of PCR primers specific to Neisseria gonorrhoeae. The primer design strategy is similar to the strategy described in Example 28.

Two N. gonorrhoeae-specific primers were selected, SEQ ID NOs. 551 and 552, which give an amplification product of 139 bp. PCR amplification was carried out on PTC-200 thermocyclers (MJ Research) using 0.4 μM of each primer as described in Example 28. The optimal cycling conditions for maximum sensitivity and specificity were as follow: three minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 65° C., followed by terminal extension at 72° C. for 2 minutes.

Specificity of the assay was tested by adding into the PCR reactions, 0.1 ng of genomic DNA from each of the following bacterial species: Neisseria gonorrhoeae (19 strains), Neisseria meningitidis (2 strains), Neisseria lactamica, Neisseria flavescens, Neisseria animalis, Neisseria canis, Neisseria cuniculi, Neisseria elongata, Neisseria mucosa, Neisseria polysaccharea, Neisseria sicca, Neisseria subflava, Neisseria weaveri. Amplification was detected only for N. gonorrhoeae, N. sicca and N. polysaccharea. The sensitivity of the assay with 40-cycle PCR was verified with two strains of N. gonorrhoeae. The detection limit for the N. gonorrhoeae strains tested was 5 copies of genomic DNA. Analysis of the multiple alignment sequence of the tuf gene allowed the design of an internal probe, SEQ ID NO. 2166, which can discriminate N. gonorrhoeae from N. sicca and N. polysaccharea.

Example 32 Sequencing of Bacterial gyrA and parC Gene Fragments. SEQUENCING of Bacterial gyrA and parC Fragments

One of the major mechanism of resistance to quinolone in various bacterial species is mediated by target changes (DNA gyrase and/or topoisomerase IV). These enzymes control DNA topology and are vital for chromosome function and replication. Each of these enzymes is a tetramer composed of two subunits: GyrA and GyrB forming A₂B₂ complex in DNA gyrase; and ParC and ParE forming and C₂E₂ complex in DNA topoisomerase IV. It has been shown that they are hotspots, called the quinolone-resistance-determining region (QRDR) for mutations within gyrA that encodes for the GyrA subunit of DNA gyrase and within parC that encodes the parC subunit of topoisomerase IV.

In order to generate a database for gyrA and parC sequences that can be used for design of primers and/or probes for the specific detection of quinolone resistance in various bacterial species, gyrA and parC DNA fragments selected from public database (GenBanK and EMBL) from a variety of bacterial species were used to design oligonucleotide primers.

Using primer pair SEQ ID NOs. 1297 and 1298, it was possible to amplify and determine gyrA sequences from Klebsiella oxytoca (SEQ ID NO. 1764), Klebsiella pneumoniae subsp. ozaneae (SEQ ID NO. 1765), Klebsiella planticola (SEQ ID NO. 1766), Klebsiella pneumoniae (SEQ ID NO. 1767), Klebsiella pneumoniae subsp. pneumoniae (two strains) (SEQ ID NOs. 1768-1769), Klebsiella pneumoniae subsp. rhinoscleromatis (SEQ ID NO. 1770), Klebsiella terrigena (SEQ ID NO. 1771), Kluyvera ascorbata (SEQ ID NO. 2013), Kluyvera georgiana (SEQ ID NO. 2014) and Escherichia coli (4 strains) (SEQ ID NOs. 2277-2280). Using primer pair SEQ ID NOs. 1291 and 1292, it was possible to amplify and determine gyrA sequences from Legionella pneumophila subsp. pneumophila (SEQ ID NO. 1772), Proteus mirabilis (SEQ ID NO. 1773), Providencia rettgeri (SEQ ID NO. 1774), Proteus vulgaris (SEQ ID NO. 1775) and Yersinia enterolitica (SEQ ID NO. 1776). Using primer pair SEQ ID NOs. 1340 and 1341, it was possible to amplify and determine gyrA sequence from Staphylococcus aureus (SEQ ID NO. 1255).

Using primers SEQ ID NOs. 1318 and 1319, it was possible to amplify and determine parC sequences from K oxytoca (two strains) (SEQ ID NOs. 1777-1778), Klebsiella pneumoniae subsp. ozaenae (SEQ ID NO. 1779), Klebsiella planticola (SEQ ID NO. 1780), Klebsiella pneumoniae (SEQ ID NO. 1781), Klebsiella pneumoniae subsp. pneumoniae (two strains) (SEQ ID NOs. 1782-1783), Klebsiella pneumoniae subsp. rhinoscleromatis (SEQ ID NO. 1784) and Klebsiella terrigena (SEQ ID NO. 1785).

Example 33 Development of a PCR Assay for the Specific Detection and Identification of Staphylococcus aureus and its Quinolone Resistance Genes gyrA and parC

The analysis of gyrA and parC sequences from a variety of bacterial species revealed conserved regions allowing the design of PCR primers specific to the quinolone-resistance-determining region (QRDR) of gyrA and parC from Staphylococcus aureus. PCR primer pair SEQ ID NOs. 1340 and 1341 was designed to amplify the gyrA sequence of S. aureus, whereas PCR primer pair SEQ ID NOs. 1342 and 1343 was designed to amplify S. aureus parC. The comparison of gyrA and parC sequences from S. aureus strains with various levels of quinolone resistance allowed the identification of amino acid substitutions Ser-84 to Leu, Glu-88 to Gly or Lys in the GyrA subunit of DNA gyrase encoded by gyrA and amino acid changes Ser-80 to Phe or Tyr and Ala-116 to Glu in the ParC subunit of topoisomerase IV encoded by parC. These amino acid substitutions in GyrA and ParC subunits occur in isolates with intermediate- or high-level quinolone resistance. Internal probes for the specific detection of wild-type S. aureus gyrA (SEQ ID NO. 1940) and wild-type S. aureus parC (SEQ ID NO. 1941) as well as internal probes for the specific detection of each of the gyrA (SEQ ID NOs. 1333-1335) and parC mutations identified in quinolone-resistant S. aureus (SEQ ID NOs. 1336-1339) were designed.

The gyrA- and parC-specific primer pairs (SEQ ID NOs. 1340-1341 and SEQ ID NOs. 1342-1343) were used in multiplex. PCR amplification was carried out on PTC-200 thermocyclers (MJ Research) using 0.3, 0.3, 0.6 and 0.6 μM of each primers, respectively, as described in Example 28. The optimal cycling conditions for maximum sensitivity and specificity were 3 minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 62° C., followed by terminal extension at 72° C. for 2 minutes. Detection of the PCR products was made by electrophoresis in agarose gels (2%) containing 0.25 μg/ml of ethidium bromide. The specificity of the multiplex assay with 40-cycle PCR was verified by using 0.1 ng of purified genomic DNA from a panel of gram-positive bacteria. The list included the following: Abiotrophia adiacens, Abiotrophia defectiva, Bacillus cereus, Bacillus mycoides, Enterococcus faecalis (2 strains), Enterococcus flavescens, Gemella morbillorum, Lactococcus lactis, Listeria innocua, Listeria monocytogenes, Staphylococcus aureus (5 strains), Staphylococcus auricalis, Staphylococcus capitis subsp. urealyticus, Staphylococcus carnosus, Staphylococcus chromogenes, Staphylococcus epidermidis (3 strains), Staphylococcus gallinarum, Staphylococcus haemolyticus (2 strains), Staphylococcus hominis, Staphylococcus hominis subsp hominis, Staphylococcuslentus, Staphylococcus lugdunensis, Staphylococcus saccharolyticus, Staphylococcus saprophyticus (3 strains), Staphylococcus simulans, Staphylococcus warneri, Staphylococcus xylosus, Streptococcus agalactiae, Streptococcus pneumoniae. Strong amplification of both gyrA and parC genes was only detected for the S. aureus strains tested. The sensitivity of the multiplex assay with 40-cycle PCR was verified with one quinolone-sensitive and four quinolone-resistant strains of S. aureus. The detection limit was 2 to 10 copies of genomic DNA, depending on the strains tested.

Detection of the hybridization with the internal probes was performed as described in Example 7. The internal probes specific to wild-type gyrA and parC of S. aureus and to the gyrA and parC variants of S. aureus were able to recognize two quinolone-resistant and one quinolone-sensitive S. aureus strains showing a perfect correlation with the susceptibility to quinolones.

The complete assay for the specific detection of S. aureus and its susceptibility to quinolone contains the Staphylococcus-specific primers (SEQ ID NOs. 553 and 575) described in Example 7 and the multiplex containing the S. aureus gyrA- and parC-specific primer pairs (SEQ ID NOs. 1340-1341 and SEQ ID NOs. 1342-1343). Amplification is coupled with post-PCR hybridization with the internal probe specific to S. aureus (SEQ ID NO. 587) described in Example 7 and the internal probes specific to wild-type S. aureus gyrA and parC (SEQ ID NOs. 1940-1941) and to the S. aureus gyrA and parC variants (SEQ ID NOs. 1333-1338).

An assay was also developed for the detection of quinolone-resistant S. aureus using the SmartCycler (Cepheid). Real-time detection is based on the use of S. aureus parC-specific primers (SEQ ID NOs. 1342 and 1343) and the Staphylococcus-specific primers (SEQ ID NOs. 553 and 575) described in Example 7. Internal probes were designed for molecular beacon detection of the wild-type S. aureus parC (SEQ ID NO. 1939), for detection of the Ser-80 to Tyr or Phe amino acid substitutions in the ParC subunit encoded by S. aureus parC (SEQ ID NOs. 1938 and 1955) and for detection of S. aureus (SEQ ID NO. 2282).

Example 34 Development of a PCR Assay for the Detection and Identification of Klebsiella pneumoniae and its Quinolone Resistance Genes gyrA and parC

The analysis of gyrA and parC sequences from a variety of bacterial species from the public databases and from the database described in Example 32 revealed conserved regions allowing the design of PCR primers specific to the quinolone-resistance-determining region (QRDR) of gyrA and parC from K. pneumoniae. PCR primer pair SEQ ID NOs. 1936 and 1937, or pair SEQ ID NOs. 1937 and 1942, were designed to amplify the gyrA sequence of K. pneumoniae, whereas PCR primer pair SEQ ID NOs. 1934 and 1935 was designed to amplify K. pneumoniae parC sequence. An alternative pair, SEQ ID NOs. 1935 and 1936, can also amplify K. pneumoniae parC. The comparison of gyrA and parC sequences from K. pneumoniae strains with various levels of quinolone resistance allowed the identification of amino acid substitutions Ser-83 to Tyr or Phe and Asp-87 to Gly or Ala and Asp-87 to Asn in the GyrA subunit of DNA gyrase encoded by gyrA and amino acid changes Ser-80 to Ile or Arg and Glu-84 to Gly or Lys in the ParC subunit of topoisomerase IV encoded by parC. These amino acid substitutions in the GyrA and ParC subunits occur in isolates with intermediate- or high-level quinolone resistance. Internal probes for the specific detection of wild-type K. pneumoniae gyrA (SEQ ID NO. 1943) and wild-type K. pneumoniae parC (SEQ ID NO. 1944) as well as internal probes for the specific detection of each of the gyrA (SEQ ID NOs. 1945-1949) and parC mutations identified in quinolone-resistant K. pneumoniae (SEQ ID NOs. 1950-1953) were designed.

Two multiplex using the K. pneumoniae gyrA- and parC-specific primer pairs were used: the first multiplex contained K. pneumoniae gyrA-specific primers (SEQ ID NOs. 1937 and 1942) and K. pneumoniae parC-specific primers (SEQ ID NOs. 1934 and 1935) and the second multiplex contained K. pneumoniae gyrA/parC-specific primer (SEQ ID NOs. 1936), K. pneumoniae gyrA-specific primer (SEQ ID NO. 1937) and K. pneumoniae parC-specific primer (SEQ ID NO. 1935). Standard PCR was carried out on PTC-200 thermocyclers (MJ Research) using for the first multiplex 0.6, 0.6, 0.4, 0.4 μM of each primer, respectively, and for the second multiplex 0.8, 0.4, 0.4 μM of each primer, respectively. PCR amplification and agarose gel electrophoresis of the amplified products were performed as described in Example 28. The optimal cycling conditions for maximum sensitivity and specificity were 3 minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 62° C., followed by terminal extension at 72° C. for 2 minutes. The specificity of the two multiplex assays with 40-cycle PCR was verified by using 0.1 ng of purified genomic DNA from a panel of gram-negative bacteria. The list included: Acinetobacter baumannii, Citrobacter freundii, Eikenella corrodens, Enterobacter aerogenes, Enterobacter cancerogenes, Enterobacter cloacae, Escherichia coli (10 strains), Haemophilus influenzae, Klebsiella pneumoniae, Klebsiella ornitholytica, Klebsiella oxytoca (2 strains), Klebsiella planticola, Klebsiella terrigena, Kluyvera ascorbata, Kluyvera cryocrescens, Kluyvera georgiana, Neisseria gonorrhoeae, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, Salmonella choleraesuis subsp. typhimurium, Salmonella enteritidis, Serratia liquefaciens, Serratia marcescens and Yersinia enterocolytica. For both multiplex, strong amplification of both gyrA and parC was observed only for the K. pneumoniae strain tested. The sensitivity of the two multiplex assays with 40-cycle PCR was verified with one quinolone-sensitive strain of K. pneumoniae. The detection limit was around 10 copies of genomic DNA.

The complete assay for the specific detection of K. pneumoniae and its susceptibility to quinolone contains the Klebsiella-specific primers (SEQ ID NOs. 1331 and 1332) described in Example 29 and either the multiplex containing the K. pneumoniae gyrA- and parC-specific primers (SEQ ID NOs. 1935, 1936, 1937) or the multiplex containing the K. pneumoniae gyrA- and parC-specific primers (SEQ ID NOs. 1934, 1937, 1939, 1942). Amplification is coupled with post-PCR hybridization with the internal probe specific to K. pneumoniae (SEQ ID NO. 2167) described in Example 29 and the internal probes specific to wild-type K. pneumoniae gyrA and parC (SEQ ID NOs. 1943, 1944) and to the K. pneumoniae gyrA and parC variants (SEQ ID NOs. 1945-1949 and 1950-1953).

An assay was also developed for the detection of quinolone-resistant K. pneumoniae using the SmartCycler (Cepheid). Real-time detection is based on the use of resistant K. pneumoniae gyrA-specific primers (SEQ ID NOs. 1936 and 1937) and the K. pneumoniae-specific primers (SEQ ID NOs. 1331 and 1332) described in Example 29. Internal probes were designed for molecular beacon detection of the wild-type K. pneumoniae gyrA (SEQ ID NO. 2251), for detection of the Ser-83 to Tyr or Phe and/or Asp-87 to Gly or Asn in the GyrA subunit of DNA gyrase encoded by gyrA (SEQ ID NOs. 2250) and for detection of K. pneumoniae (SEQ ID NO. 2281).

Example 35 Development of a PCR Assay for Detection and Identification of S. pneumoniae and its Quinolone Resistance Genes gyrA and parC

The analysis of gyrA and parC sequences from a variety of bacterial species revealed conserved regions allowing the design of PCR primers able to amplify the quinolone-resistance-determining region (QRDR) of gyrA and parC from all S. pneumoniae strains. PCR primer pair SEQ ID NOs. 2040 and 2041 was designed to amplify the QRDR of S. pneumoniae gyrA, whereas PCR primer pair SEQ ID NOs. 2044 and 2045 was designed to amplify the QRDR of S. pneumoniae parC. The comparison of gyrA and parC sequences from S. pneumoniae strains with various levels of quinolone resistance allowed the identification of amino acid substitutions Ser-81 to Phe or Tyr in the GyrA subunit of DNA gyrase encoded by gyrA and amino acid changes Ser-79 to Phe in the ParC subunit of topoisomerase IV encoded by parC. These amino acid substitutions in the GyrA and ParC subunits occur in isolates with intermediate- or high-level quinolone resistance. Internal probes for the specific detection of each of the gyrA (SEQ ID NOs. 2042 and 2043) and parC (SEQ ID NO. 2046) mutations identified in quinolone-resistant S. pneumoniae were designed.

For all bacterial species, amplification was performed from purified genomic DNA. 1 μl of genomic DNA at 0.1 ng/μL was transferred directly to a 19 μl PCR mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 0.4 μM (each) of the above primers SEQ ID NOs. 2040, 2041, 2044 and 2045, 0.05 mM bovine serum albumin (BSA) and 0.5 U Taq polymerase coupled with TaqStart™ antibody. The optimal cycling conditions for maximum sensitivity' and specificity were 3 minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 58° C., followed by terminal extension at 72° C. for 2 minutes. In order to generate Digoxigenin (DIG)-labeled amplicons for capture probe hybridization, 0.1×PCR DIG labeling four deoxynucleoside triphosphates mix (Boehringer Mannheim GmbH) was used for amplification.

The DIG-labeled amplicons were hybridized to the capture probes bound to 96-well plates. The plates were incubated with anti-DIG-alkaline phosphatase and the chemiluminescence was measured by using a luminometer (MLX, Dynex Technologies Inc.) after incubation with CSPD and recorded as Relative Light Unit (RLU). The RLU ratio of tested sample with and without captures probes was then calculated. A ratio 2.0 was defined as a positive hybridization signal. All reactions were performed in duplicate.

The specificity of the multiplex assay with 40-cycle PCR was verified by using 0.1 ng of purified genomic DNA from a panel of bacteria listed in Table 13. Strong amplification of both gyrA and parC was detected only for the S. pneumoniae strains tested. Weak amplification of both gyrA and parC genes was detected for Staphylococcus simulans. The detection limit tested with purified genomic DNA from 5 strains of S. pneumoniae was 1 to 10 genome copies. In addition, 5 quinolone-resistant and 2 quinolone-sensitive clinical isolates of S. pneumoniae were tested to further validate the developed multiplex PCR coupled with capture probe hybridization assays. There was a perfect correlation between detection of S. pneumoniae gyrA and parC mutations and the susceptibility to quinolone.

The complete assay for the specific detection of S. pneumoniae and its susceptibility to quinolone contains the S. pneumoniae-specific primers (SEQ ID NOs. 1179 and 1181) described in Example 20 and the multiplex containing the S. pneumoniae gyrA-specific and parC-specific primer pairs (SEQ ID NOS. 2040 and 2041 and SEQ ID NOs. 2044 and 2045). Amplification is coupled with post-PCR hybridization with the internal probe specific to S. pneumoniae (SEQ ID NO. 1180) described in Example and the internal probes specific to each of the S. pneumoniae gyrA and parC variants (SEQ ID NOs. 2042, 2043 and 2046).

Example 36 Detection of Extended-Spectrum TEM-Type β-Lactamases in Escherichia coli

The analysis of TEM sequences which confer resistance to third-generation cephalosporins and to β-lactamase inhibitors allowed the identification of amino acid substitutions Met-69 to Ile or Leu or Val, Ser-130 to Gly, Arg-164 to Ser or His, Gly-238 to Ser, Glu-240 to Lys and Arg-244 to Ser or Cys or Thr or His or Leu. PCR primers SEQ ID NOs. 1907 and 1908 were designed to amplify TEM sequences. Internal probes for the specific detection of wild-type TEM (SEQ ID NO. 2141) and for each of the amino acid substitutions (SEQ ID NOs. 1909-1926) identified in TEM variants were designed to detect resistance to third-generation cephalosporins and to β-lactamase inhibitors. Design and synthesis of primers and probes, and detection of the hybridization were performed as described in Example 7.

For all bacterial species, amplification was performed from purified genomic DNA. One μl of genomic DNA at 0.1 ng/μl was transferred directly to a 19 μl PCR mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0); 0.1% Triton X-100, 2.5 mM MgCl₂, 0.4 μM of the TEM-specific primers SEQ ID NOs. 1907 and 1908, 200 μM (each) of the four deoxynucleoside triphosphates, 0.05 mM bovine serum albumin (BSA) and 0.5 U Taq polymerase (Promega) coupled with TaqStart™ antibody. PCR amplification and agarose gel analysis of the amplified products were performed as described in Example 28. The optimal cycling conditions for maximum sensitivity and specificity were 3 minutes at 95° C. for initial denaturation, then forty cycles of three steps consisting of 5 seconds at 95° C., 30 seconds at 55° C. and 30 seconds at 72° C., followed by terminal extension at 72° C. for 2 minutes.

The specificity of the TEM-specific primers with 40-cycle PCR was verified by using 0.1 ng of purified genomic from the following bacteria: three third-generation cephalosporin-resistant Escherichia coli strains (one with TEM-10, one with TEM-28 and the other with TEM-49), two third-generation cephalosporin-sensitive Escherichia coli strain (one with TEM-1 and the other without TEM), one third-generation cephalosporin-resistant Klebsiella pneumoniae strain (with TEM-47), and one β-lactamase-inhibitor-resistant Proteus mirabilis strain (with TEM-39). Amplification with the TEM-specific primers was detected only for strains containing TEM.

The sensitivity of the assay with 40-cycle PCR was verified with three E. coli strains containing TEM-1 or TEM-10 or TEM-49, one K. pneumoniae strain containing TEM-47 and one P. mirabilis strain containing TEM-39. The detection limit was 5 to 100 copies of genomic DNA, depending on the TEM-containing strains tested.

The TEM-specific primers SEQ ID NOs. 1907 and 1908 were used in multiplex with the Escherichia coli/Shigella sp.-specific primers SEQ ID NOs. 1661 and 1665 described in Example 28 to allow the complete identification of Escherichia coli/Shigella sp. and the susceptibility to β-lactams. PCR amplification with 0.4 μM of each of the primers and agarose gel analysis of the amplified products was performed as described above.

The specificity of the multiplex with 40-cycle PCR was verified by using 0.1 ng of purified genomic DNA from the following bacteria: three third-generation cephalosporin-resistant Escherichia coli strains (one with TEM-10, one with TEM-28 and the other with TEM-49), two third-generation cephalosporin-sensitive Escherichia coli strain (one with TEM-1 and the other without TEM), one third-generation cephalosporin-resistant Klebsiella pneumoniae strain (with TEM-47), and one β-lactamase-inhibitor-resistant Proteus mirabilis strain (with TEM-39). The multiplex was highly specific to Escherichia coli strains containing TEM.

The complete assay for detection of TEM-type β-lactamases in E. coli includes PCR amplification using the multiplex containing the TEM-specific primers (SEQ ID NOs. 1907 and 1908) and the Escherichia coli/Shigella sp.-specific primers (SEQ ID NOs. 1661 and 1665) coupled with post PCR-hybridization with the internal probes specific to wild-type TEM (SEQ ID NO. 2141) and to the TEM variants (SEQ ID NOs. 1909-1926).

Example 37 Detection of Extended-Spectrum SHY-Type β-Lactamases in Klebsiella pneumoniae

The comparison of SHV sequences, which confer resistance to third-generation cephalosporins and to β-lactamase inhibitors, allowed the identification of amino acid substitutions Ser-130 to Gly, Asp-179 to Ala or Asn, Gly-238 to Ser, and Glu-240 to Lys. PCR primer pair SEQ ID NOs. 1884 and 1885 was designed to amplify SHV sequences. Internal probes for the specific identification of wild-type SHV (SEQ ID NO. 1896) and for each of the amino acid substitutions (SEQ ID NOs. 1886-1895 and 1897-1898) identified in SHV variants were designed to detect resistance to third-generation cephalosporins and to β-lactamase inhibitors. Design and synthesis of primers and probes, and detection of the hybridization were performed as described in Example 7.

For all bacterial species, amplification was performed from purified genomic DNA. One μl of genomic DNA at 0.1 ng/μl was transferred directly to a 19 μl PCR mixture. Each PCR reaction contained 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 0.4 μM of the SHV-specific primers SEQ ID NO. 1884 and 1885, 200 μM (each) of the four deoxynucleoside triphosphates, 0.05 mM bovine serum albumin (BSA) and 0.5 U Taq polymerase (Promega) coupled with TaqStart™ antibody. PCR amplification and agarose gel analysis of the amplified products were performed as described in Example 28. The optimal cycling conditions for maximum sensitivity and specificity were 3 minutes at 95° C. for initial denaturation, then forty cycles of three steps consisting of 5 seconds at 95° C., 30 seconds at 55° C. and 30 seconds at 72° C., followed by terminal extension at 72° C. for 2 minutes.

The specificity of the SHV-specific primers with 40-cycle PCR was verified by using 0.1 ng of purified genomic from the following bacteria: two third-generation cephalosporin-resistant Klebsiella pneumoniae strains (one with SHV-2a and the other with SHV-12), one third-generation cephalosporin-sensitive Klebsiella pneumoniae strain (with SHV-1), two third-generation cephalosporin-resistant Escherichia coli strains (one with SHV-8 and the other with SHV-7), and two third-generation cephalosporin-sensitive Escherichia coli strains (one with SHV-1 and the other without any SHV). Amplification with the SHV-specific primers was detected only for strains containing SHV.

The sensitivity of the assay with 40-cycle PCR was verified with four strains containing SHV. The detection limit was 10 to 100 copies of genomic DNA, depending on the SHV-containing strains tested.

The amplification was coupled with post-PCR hybridization with the internal probes specific for identification of wild-type SHV (SEQ ID NO. 1896) and for each of the amino acid substitutions (SEQ ID NOs. 1886-1895 and 1897-1898) identified in SHV variants. The specificity of the probes was verified with six strains containing various SHV enzymes, one Klebsiella pneumoniae strain containing SHV-1, one Klebsiella pneumoniae strain containing SHV-2a, one Klebsiella pneumoniae strain containing SHV-12, one Escherichia coli strain containing SHV-1, one Escherichia coli strain containing SHV-7 and one Escherichia coli strain containing SHV-8. The probes correctly detected each of the SHV genes and their specific mutations. There was a perfect correlation between the SHV genotype of the strains and the susceptibility to β-lactam antibiotics.

The SHV-specific primers SEQ ID NOs. 1884 and 1885 were used in multiplex with the K. pneumoniae-specific primers SEQ ID NOs. 1331 and 1332 described in Example 29 to allow the complete identification of K. pneumoniae and the susceptibility to β-lactams. PCR amplification with 0.4 μM of each of the primers and agarose gel analysis of the amplified products were performed as described above.

The specificity of the multiplex with 40-cycle PCR was verified by using 0.1 ng of purified genomic DNA from the following bacteria: three K. pneumoniae strains containing SHV-1, one Klebsiella pneumoniae strain containing SHV-2a, one Klebsiella pneumoniae strain containing SHV-12, one K. rhinoscleromatis strain containing SHV-1, one Escherichia coli strain without SHV. The multiplex was highly specific to Klebsiella pneumoniae strain containing SHV.

Example 38 Development of a PCR Assay for the Detection and Identification of Neisseria gonorrhoeae and its associated tetracycline resistance gene tetM

The analysis of publicly available tetM sequences revealed conserved regions allowing the design of PCR primers specific to tetM sequences. The PCR primer pair SEQ ID NOs. 1588 and 1589 was used in multiplex with the Neisseria gonorrhoeae-specific primers SEQ ID NOs. 551 and 552 described in Example 31. Sequence alignment analysis of tetM sequences revealed regions suitable for the design of an internal probe specific to tetM (SEQ ID NO. 2254). PCR amplification was carried out on PTC-200 thermocyclers (MJ Research) using 0.4 μM of each primer pair as described in Example 28. The optimal cycling conditions for maximum sensitivity and specificity were as follow: three minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 60° C., followed by terminal extension at 72° C. for 2 minutes.

The specificity of the multiplex PCR assay with 40-cycle PCR was verified by using 0.1 ng of purified genomic DNA from the following bacteria: two tetracycline-resistant Escherichia coli strains (one containing the tetracycline-resistant gene tetB and the other containing the tetracycline-resistant gene tetC), one tetracycline-resistant Pseudomonas aeruginosa strain (containing the tetracycline-resistant gene tetA), nine tetracycline-resistant Neisseria gonorrhoeae strains, two tetracycline-sensitive Neisseria meningitidis strains, one tetracycline-sensitive Neisseria polysaccharea strain, one tetracycline-sensitive Neisseria sicca strain and one tetracycline-sensitive Neisseria subflava strain. Amplification with both the tetM-specific and Neisseria gonorrhoeae-specific primers was detected only for N. gonorrhoeae strains containing tetM. There was a weak amplification signal using Neisseria gonorrhoeae-specific primers for the following species: Neisseria sicca, Neisseria polysaccharea and Neisseria meningitidis. There was a perfect correlation between the tetM genotype and the tetracycline susceptibility pattern of the Neisseria gonorrhoeae strains tested. The internal probe specific to N. gonorrhoeae SEQ ID NO. 2166 described in Example 31 can discriminate Neisseria gonorrhoeae from the other Neisseria sp.

The sensitivity of the assay with 40-cycle PCR was verified with two tetracycline resistant strains of N. gonorrhoeae. The detection limit was 5 copies of genomic DNA for both strains.

Example 39 Development of a PCR Assay for the Detection and Identification of Shigella Sp. and their Associated Trimethoprim Resistance Gene dhfrIa

The analysis of publicly available dhfrIa and other dhfr sequences revealed regions allowing the design of PCR primers specific to dhfrIa sequences. The PCR primer pair (SEQ ID NOs. 1459 and 1460) was used in multiplex with the Escherichia coli/Shigella sp.-specific primers SEQ ID NOs. 1661 and 1665 described in Example 28. Sequence alignment analysis of dhfrIa sequences revealed regions suitable for the design of an internal probe specific to dhfrIa (SEQ ID NO. 2253). PCR amplification and agarose gel analysis of the amplified products were performed as described in Example 28 with an annealing temperature of 60° C. The specificity of the multiplex assay with 40-cycle PCR was verified by using 0.1 ng of purified genomic DNA from a panel of bacteria. The list included the following trimethoprim-sensitive strains, Salmonella typhimyurium, Salmonella typhi, Salmonella enteritidis, Tatumella ptyseos, Klebsiella pneumoniae, Enterobacter aerogenes, Citrobacter farmeri, Campylobacter jejuni, Serratia marcescens, Shigella dysenteriae, Shigella flexneri, Shigella sonnei, six trimethoprim-resistant Escherichia coli strains (containing dhfrIa or dhfrV or dhfrVII or dhfrXII or dhfrXIII or dhfrXV), four trimethoprim-resistant strains containing dhfrIa (Shigella sonnei, Shigella flexneri, Shigella dysenteriae and Escherichia coli). There was a perfect correlation between the dhfrIa genotype and the trimethoprim susceptibility pattern of the Escherichia coli and Shigella sp. strains tested. The dhfrIa primers were specific to the dhfrIa gene and did not amplify any of the other trimethoprim-resistant dhfr genes tested. The sensitivity of the multiplex assay with 40-cycle PCR was verified with three strains of trimethoprim-resistant strains of Shigella sp. The detection limit was 5 to 10 genome copies of DNA, depending on the Shigella sp. strains tested.

Example 40 Development of a PCR Assay for the Detection and Identification of Acinetobacter baumannii and its Associated Aminoglycoside Resistance Gene aph(3′)-VIa

The comparison of publicly available aph(3′)-VIa sequence revealed regions allowing the design of PCR primers specific to aph(3)-VIa. The PCR primer pair (SEQ ID NOs. 1404 and 1405) was used in multiplex with the Acinetobacter baumannii-specific primers SEQ ID NOs. 1692 and 1693 described in Example 30. Analysis of the aph(3)-VIa sequence revealed region suitable for the design of an internal probe specific to aph(3′)-VIa (SEQ ID NO. 2252). PCR amplification and agarose gel analysis of the amplified products were performed as described in Example 28. The specificity of the multiplex assay with 40-cycle PCR was verified by using 0.1 ng of purified genomic DNA from a panel of bacteria including: two aminoglycoside-resistant A. baumanni strains (containing aph(3)-VIa), one aminoglycoside-sensitive A. baumani strain, one of each of the following aminoglycoside-resistant bacteria, one Serratia marcescens strain containing the aminoglycoside-resistant gene aacC1, one Serratia marcescens strain containing the aminoglycoside-resistant gene aacC4, one Enterobacter cloacae strain containing the aminoglycoside-resistant gene aacC2, one Enterococcus faecalis containing the aminoglycoside-resistant gene aacA-aphD, one Pseudomonas aeruginosa strain containing the aminoglycoside-resistant gene aac6IIa and one of each of the following aminoglycoside-sensitive bacterial species, Acinetobacter anitratus, Acinetobacter lwoffi, Psychobbacter phenylpyruvian, Neisseria gonorrhoeae, Haemophilus haemolyticus, Haemophilus influenzae, Yersinia enterolitica, Proteus vulgaris, Eikenella corrodens, Escherichia coli. There was a perfect correlation between the aph(3′)-VIa genotype and the aminoglycoside susceptibility pattern of the A. baumannii strains tested. The aph(3)-VIa-specific primers were specific to the aph(3)-VIa gene and did not amplify any of the other aminoglycoside-resistant genes tested. The sensitivity of the multiplex assay with 40-cycle PCR was verified with two strains of aminoglycoside-resistant strains of A. baumannii. The detection limit was 5 genome copies of DNA for both A. baumannii strains tested.

Example 41 Specific Identification of Bacteroides fragilis Using atpD (V-Type) Sequences

The comparison of atpD (V-type) sequences from a variety of bacterial species allowed the selection of PCR primers for Bacteroides fragilis. The strategy used to design the PCR primers was based on the analysis of a multiple sequence alignment of various atpD sequences from B. fragilis, as well as atpD sequences from the related species B. dispar, bacterial genera and archaea, especially representatives with phylogenetically related atpD sequences. A careful analysis of this alignment allowed the selection of oligonucleotide sequences which are conserved within the target species but which discriminate sequences from other species, especially from closely related species B. dispar, thereby permitting the species-specific and ubiquitous detection and identification of the target bacterial species.

The chosen primer pair, SEQ ID NOs. 2134-2135, produces an amplification product of 231 bp. Standard PCR was carried out on PTC-200 thermocyclers (MJ Research Inc.) using 0.4 μM of each primers pair as described in Example 28. The optimal cycling conditions for maximum sensitivity and specificity were as follows: three minutes at 95° C. for initial denaturation, then forty cycles of two steps consisting of 1 second at 95° C. and 30 seconds at 60° C., followed by terminal extension at 72° C. for 2 minutes.

The format of this assay is not limited to the one described above. A person skilled in the art could adapt the assay for different formats such as PCR with real-time detection using molecular beacon probes. Molecular beacon probes designed to be used in this assay include, but are not limited to, SEQ ID NO. 2136 for the detection of the B. fragilis amplicon.

Example 42 Evidence for Horizontal Gene Transfer in the Evolution of the Elongation Factor Tu in Enterococci Overview

The elongation factor Tu, encoded by tuf genes, is a GTP binding protein that plays a central role in protein synthesis. One to three tuf genes per genome are present depending on the bacterial species. Most low G+C gram-positive bacteria carry only one tuf gene. We have designed degenerate PCR primers derived from consensus sequences of the tuf gene to amplify partial tuf sequences from 17 enterococcal species and other phylogenetically related species. The amplified DNA fragments were sequenced either by direct sequencing or by sequencing cloned inserts containing putative amplicons. Two different tuf genes (tufA and tufB) were found in 11 enterococcal species, including Enterococcus avium, E. casseliflavus, E. dispar, E. durans, E. faecium, E. gallinarum, E. hirae, E. malodoratus, E. mundtii, E. pseudoavium, and E. raffinosus. For the other six enterococcal species (E. cecorum, E. columbae, E. faecalis, E. sulfureus, E. saccharolyticus, and E. solitarius), only the tufA gene was present. Based on 16S rRNA gene sequence analysis, the 11 species having two tuf genes all share a common ancestor, while the six species having only one copy diverged from the enterococcal lineage before that common ancestor. The presence of one or two copies of the tuf gene in enterococci was confirmed by Southern hybridization. Phylogenetic analysis of tuf sequences demonstrated that the enterococcal tufA gene branches with the Bacillus, Listeria and Staphylococcus genera, while the enterococcal tufB gene clusters with the genera Streptococcus and Lactococcus. Primary structure, analysis showed that four amino acid residues within the sequenced regions are conserved and unique to the enterococcal tufB genes and the tuf genes of streptococci and L. lactis. The data suggest that an ancestral streptococcus or a streptococcus-related species may have horizontally transferred a tuf gene to the common ancestor of the 11 enterococcal species which now carry two tuf genes.

Introduction

The elongation factor Tu (EF-Tu) is a GTP binding protein playing a central role in protein synthesis. It mediates the recognition and transport of aminoacyl-tRNAs and their positioning to the A-site of the ribosome. The highly conserved function and ubiquitous distribution render the elongation factor a valuable phylogenetic marker among eubacteria and even throughout the archaebacterial and eukaryotic kingdoms. The tuf genes encoding elongation factor Tu are present in various copy numbers per bacterial genome. Most gram-negative bacteria contain two tuf genes. As found in Escherichia coli, the two genes, while being almost identical in sequence, are located in different parts of the bacterial chromosome. However, recently completed microbial genomes revealed that only one tuf gene is found in Helicobacter pylori as well as in some obligate parasitic bacteria, such as Borrelia burgdorferi, Rickettsia prowazekii, and Treponema pallidum, and in some cyanobacteria. In most gram-positive bacteria studied so far, only one tuf gene was found. However, Southern hybridization showed that there are two tuf genes in some clostridia as well as in Streptomyces coelicolor and S. lividans. Up to three tuf-like genes have been identified in S. ramocissimus.

Although massive prokaryotic gene transfer is suggested to be one of the factors responsible for the evolution of bacterial genomes, the genes encoding components of the translation machinery are thought to be highly conserved and difficult to be transferred horizontally due to the complexity of their interactions. However, a few recent studies demonstrated evidence that horizontal gene transfer has also occurred in the evolution of some genes coding for the translation apparatus, namely, 16S rRNA and some aminoacyl-tRNA synthetases. No further data suggest that such a mechanism is involved in the evolution of the elongation factors. Previous studies concluded that the two copies of tuf genes in the genomes of some bacteria resulted from an ancient event of gene duplication. Moreover, a study of the tuf gene in R. prowazekii suggested that intrachromosomal recombination has taken place in the evolution of the genome of this organism.

To date, little is known about the tuf genes of enterococcal species. In this study, we analyzed partial sequences of tuf genes in 17 enterococcal species, namely, E. avium, E. casseliflavus, E. cecorum, E. columbae, E. dispar, E. durans, E. faecalis, E. faecium, E. gallinarum, E. hirae, E. malodoratus, E. mundtii, E. pseudoavium, E. raffinosus, E. saccharolyticus, E. solitarius, and E. sulfureus. We report here the presence of two divergent copies of tuf genes in 11 of these enterococcal species. The 6 other species carried a single tuf gene. The evolutionary implications are discussed.

Materials and Methods

Bacterial strains. Seventeen enterococcal strains and other gram-positive bacterial strains obtained from the American Type Culture Collection (ATCC, Manassas, Va.) were used in this study (Table 16). All strains were grown on sheep blood agar or in brain-heart infusion broth prior to DNA isolation.

DNA isolation. Bacterial DNAs were prepared using the G NOME DNA extraction kit (Bio101, Vista, Calif.) as previously described.

Sequencing of putative tuf genes. In order to obtain the tuf gene sequences of enterococci and other gram-positive bacteria, two sequencing approaches were used: 1) sequencing of cloned PCR products and 2) direct sequencing of PCR products. A pair of degenerate primers (SEQ ID NOs. 664 and 697) were used to amplify an 886-bp portion of the tuf genes from enterococcal species and other gram-positive bacteria as previously described. For E. avium, E. casseliflavus, E. dispar, E. durans, E. faecium, E. gallinarum, E. hirae, E. mundtii, E. pseudoavium, and E. raffinosus, the amplicons were cloned using the Original TA cloning kit (Invitrogen, Carlsbad, Calif.) as previously described. Five clones for each species were selected for sequencing. For E. cecorum, E. faecalis, E. saccharolyticus, and E. solitarius as well as the other gram-positive bacteria, the sequences of the 886-bp amplicons were obtained by direct sequencing. Based on the results obtained from the earlier rounds of sequencing, two pairs of primers were designed for obtaining the partial tuf sequences from the other enterococcal species by direct sequencing. One pair of primers (SEQ ID NOs. 543 and 660) were used to amplify the enterococcal tuf gene fragments from E. columbae, E. malodoratus, and E. sulfureus. Another pair of primers (SEQ ID NOs. 664 and 661) were used to amplify the second tuf gene fragments from E. avium, E. malodoratus, and E. pseudoavium.

Prior to direct sequencing, PCR products were electrophoresed on 1% agarose gel at 120V for 2 hours. The gel was then stained with 0.02% methylene blue for 30 minutes and washed twice with autoclaved distilled water for 15 minutes. The gel slices containing PCR products of the expected sizes were cut out and purified with the QIAquick gel extraction kit (QIAgen Inc., Mississauga, Ontario, Canada) according to the manufacturer's instructions. PCR mixtures for sequencing were prepared as described previously. DNA sequencing was carried out with the Big Dye™ Terminator Ready Reaction cycle sequencing kit using a 377 DNA sequencer (PE Applied Biosystems, Foster City, Calif.). Both strands of the amplified DNA were sequenced. The sequence data were verified using the Sequencer™ 3.0 software (Gene Codes Corp., Ann Arbor, Mich.).

Sequence analysis and phylogenetic study. Nucleotide sequences of the tuf genes and their respective flanking regions for E. faecalis, Staphylococcus aureus, and Streptococcus pneumoniae, were retrieved from the TIGR microbial genome database and S. pyogenes from the University of Oklahoma database. DNA sequences and deduced protein sequences obtained in this study were compared with those in all publicly available databases using the BLAST and FASTA programs. Unless specified, sequence analysis was conducted with the programs from GCG package (Version 10; Genetics Computer Group, Madison, Wis.). Sequence alignment of the tuf genes from 74 species representing all three kingdoms of life (Tables 16 and 17) were carried out by use of Pileup and corrected upon visual analysis. The N- and C-termini extremities of the sequences were trimmed to yield a common block of 201 amino acids sequences and equivocal residues were removed. Phylogenetic analysis was performed with the aid of PAUP 4.0b4 written by Dr. David L. Swofford (Sinauer Associates, Inc., Publishers, Sunderland, Mass.). The distance matrix and maximum parsimony were used to generate phylogenetic trees and bootstrap resampling procedures were performed using 500 and 100 replications in each analysis, respectively.

Protein structure analysis. The crystal structures of (i)Thermus aquaticus EF-Tu in complex with Phe-tRNA^(Phe) and a GTP analog and (ii) E. coli EF-Tu in complex with GDP served as templates for constructing the equivalent models for enterococcal EF-Tu. Homology modeling of protein structure was performed using the SWISS-MODEL server and inspected using the SWISS-PDB viewer version 3.1.

Southern hybridization. In a previous study, we amplified and cloned an 803-bp PCR product of the tuf gene fragment from E. faecium. Two divergent sequences of the inserts, which we assumed to be tufA and tufB genes, were obtained. The recombinant plasmid carrying either tufA or tufB sequence was used to generate two probes labeled with Digoxigenin (DIG)-11-dUTP by PCR incorporation following the instructions of the manufacturer (Boehringer Mannheim, Laval, Québec, Canada). Enterococcal genomic DNA samples (1-2 μg) were digested to completion with restriction endonucleases BglII and XbaI as recommended by the supplier (Amersham Pharmacia Biotech, Mississauga, Ontario, Canada). These restriction enzymes were chosen because no restriction sites were observed within the amplified tuf gene fragments of most enterococci. Southern blotting and filter hybridization were performed using positively charged nylon membranes (Boehringer Mannheim) and QuikHyb hybridization solution (Stratagene Cloning Systems, La Jolla, Calif.) according to the manufacturers' instructions with modifications. Twenty μl of each digestion were electrophoresed for 2 h at 120V on a 0.8% agarose gel. The DNA fragments were denatured with 0.5 M NaOH and transferred by Southern blotting onto a positively charged nylon membrane (Boehringer Mannheim). The filters were pre-hybridized for 15 min and then hybridized for 2 h in the QuikHyb solution at 68° C. with either DIG-labeled probe. Posthybridization washings were performed twice with 0.5×SSC, 1% SDS at room temperature for 15 min and twice in the same solution at 60° C. for 15 min. Detection of bound probes was achieved using disodium 3-(4-methoxyspiro(1,2-dioxetane-3,2′-(5′-chloro) tricyclo(3,3.1.1^(3.7)) decan)-4-yl) phenyl phosphate (CSPD) (Boehringer Mannheim) as specified by the manufacturer.

GenBank submission. The GenBank accession numbers for partial tuf gene sequences generated in this study are given in Table 16.

Results

Sequencing and nucleotide sequence analysis. In this study, all gram-positive bacteria other than enterococci yielded a single tuf sequence of 886 by using primers SEQ ID NOs. 664 and 697 (Table 16). Each of four enterococcal species including E. cecorum, E. faecalis, E. saccharolyticus, and E. solitarius also yielded one 886-bp tuf sequence. On the other hand, for E. avium, E. casseliflavus, E. dispar, E. durans, E. faecium, E. gallinarum, E. hirae, E. mundtii, E. pseudoavium, and E. raffinosus, direct sequencing of the 886-bp fragments revealed overlapping peaks according to their sequence chromatograms, suggesting the presence of additional copies of the tuf gene. Therefore, the tuf gene fragments of these 10 species were cloned first and then sequenced. Sequencing data revealed that two different types of tuf sequences (tufA and tufB) are found in eight of these species including E. casseliflavus, E. dispar, E. durans, E. faecium, E. gallinarum, E. hirae, E. mundtii, and E. raffinosus. Five clones from E. avium and E. pseudoavium yielded only a single tuf sequence. These new sequence data allowed the design of new primers specific for the enterococcal tufA or tufB sequences. Primers SEQ ID NOs. 543 and 660 were designed to amplify only enterococcal tufA sequences and a 694-bp fragment was amplified from all 17 enterococcal species. The 694-bp sequences of tufA genes from E. columbae, E. malodoratus, and E. sulfureus were obtained by direct sequencing using these primers. Primers SEQ ID NOs. 664 and 661 were designed for the amplification of 730-bp portion of tufB genes and yielded the expected fragments from 11 enterococcal species, including E. malodoratus and the 10 enterococcal species in which heterogeneous tuf sequences were initially found. The sequences of the tufB fragments for E. avium, E. malodoratus and E. pseudoavium were determined by direct sequencing using the primers SEQ ID NOs. 664 and 661. Overall, tufA gene fragments were obtained from all 17 enterococcal species but tufB gene fragments were obtained with only 11 enterococcal species (Table 16).

The identities between tufA and tufB for each enterococcal species were 68-79% at the nucleotide level and 81 to 89% at the amino acid level. The tufA gene is highly conserved among all enterococcal species with identities varying from 87% to 99% for DNA and 93% to 99% for amino acid sequences, while the identities among tufB genes of enterococci varies from 77% to 92% for DNA and 91% to 99% for amino acid sequences, indicating their different origins and evolution (Table 18). Since E. solitarius has been transferred to the genus Tetragenococcus, which is also a low G+C gram-positive bacterium, our sequence comparison did not include this species as an enterococcus. G+C content of enterococcal tufA sequences ranged from 40.8% to 43.1%, while that of enterococcal tufB sequences varied from 37.8% to 46.3%. Based on amino acid sequence comparison, the enterococcal tufA gene products share higher identities with those of Abiotrophia adiacens, Bacillus subtilis, Listeria monocytogenes, S. aureus, and S. epidermidis. On the other hand, the enterococcal tufB gene products share higher percentages of amino acid identity with the tuf genes of S. pneumoniae, S. pyogenes and Lactococcus lactis (Table 18).

In order to elucidate whether the two enterococcal tuf sequences encode genuine EF-Tu, the deduced amino acid sequences of both genes were aligned with other EF-Tu sequences available in SWISSPROT (Release 38). Sequence alignment demonstrated that both gene products are highly conserved and carry all conserved residues present in this portion of prokaryotic EF-Tu (FIG. 4). Therefore, it appears that both gene products could fulfill the function of EF-Tu. The partial tuf gene sequences encode the portion of EF-Tu from residues 117 to 317, numbered as in E. coli. This portion makes up of the last four α-helices and two β-strands of domain I, the entire domain II and the N-terminal part of domain III on the basis of the determined structures of E. coli EF-Tu.

Based on the deduced amino acid sequences, the enterococcal tufB genes have unique conserved residues Lys129, Leu140, Ser230, and Asp234 (E. coli numbering) that are also conserved in streptococci and L. lactis, but not in the other bacteria (FIG. 4). All these residues are located in loops except for Ser230. In other bacteria the residue Ser230 is substituted for highly conserved Thr, which is the 5^(th) residue of the third β-strand of domain II. This region is partially responsible for the interaction between the EF-Tu and aminoacyl-tRNA by the formation of a deep pocket for any of the 20 naturally occurring amino acids. According to our three-dimensional model (data not illustrated), the substitution Thr230→Ser in domain II of EF-Tu may have little impact on the capability of the pocket to accommodate any amino acid. However, the high conservation of Thr230 comparing to the unique Ser substitution found only. in streptococci and 11 enterococci could suggest a subtle functional role for this residue.

The tuf gene sequences obtained for E. faecalis, S. aureus, S. pneumoniae and S. pyogenes were compared with their respective incomplete genome sequence. Contigs with more than 99% identity were identified. Analysis of the E. faecalis genome data revealed that the single E. faecalis tuf gene is located within an str operon where tuf is preceded by fus that encodes the elongation factor G. This str operon is present in S. aureus and B. subtilis but not in the two streptococcal genomes examined. The 700-bp or so sequence upstream the S. pneumoniae tuf gene has no homology with any known gene sequences. In S. pyogenes, the gene upstream of tuf is similar to a cell division gene, ftsW, suggesting that the tuf genes in streptococci are not arranged in a str operon.

Phylogenetic analysis. Phylogenetic analysis of the tuf amino acid sequences with representatives of eubacteria, archeabacteria, and eukaryotes using neighbor-joining and maximum parsimony methods showed three major clusters representing the three kingdoms of life. Both methods gave similar topologies consistent with the rRNA gene data (data not shown). Within the bacterial clade, the tree is polyphyletic but tufA genes from all enterococcal species always clustered with those from other low G+C gram-positive bacteria (except for streptococci and lactococci), while the tufB genes of the 11 enterococcal species form a distinct cluster with streptococci and L. lactis (FIG. 5). Duplicated genes from the same organism do not cluster together, thereby not suggesting evolution by recent gene duplication.

Southern hybridization. Southern hybridization of BglII/XbaI digested genomic DNA from 12 enterococcal species tested with the tufA probe (DIG-labeled tufA fragment from E. faecium) yielded two bands of different sizes in 9 species, which also carried two divergent tuf sequences according to their sequencing data. For E. faecalis and E. solitarius, a single band was observed indicating that one tuf gene is present (FIG. 6). A single band was also found when digested genomic DNA from S. aureus, S. pneumoniae, and S. pyogenes were hybridized with the tufA probe (data not shown). For E. faecium, the presence of three bands can be explained by the existence of a XbaI restriction site in the middle of the tufA sequence, which was confirmed by sequencing data. Hybridization with the tufB probe (DIG-labeled tufB fragment of E. faecium) showed a banding profile similar to the one obtained with the tufA probe (data not shown).

Discussion

In this study, we have shown that two divergent copies of genes encoding the elongation factor Tu are present in some enterococcal species. Sequence data revealed that both genes are highly conserved at the amino acid level. One copy (tufA) is present in all enterococcal species, while the other (tufB) is present only in 11 of the 17 enterococcal species studied. Based on 16S rRNA sequence analysis, these 11 species are members of three different enterococcal subgroups (E. avium, E. faecium, and E. gallinarum species groups) and a distinct species (E. dispar). Moreover, 16S rDNA phylogeny suggests that these 11 species possessing 2 tuf genes all share a common ancestor before they further evolved to become the modern species. Since the six other species having only one copy diverged from the enterococcal lineage before that common ancestor, it appears that the presence of one tuf gene in these six species is not attributable to gene loss.

Two clusters of low G+C gram-positive bacteria were observed in the phylogenetic tree of the tuf genes: one contains a majority of low G+C gram-positive bacteria and the other contains lactococci and streptococci. This is similar to the finding on the basis of phylogenetic analysis of the 16S rRNA gene and the hrcA gene coding for a unique heat-shock regulatory protein. The enterococcal tufA genes branched with most of the low G+C gram-positive bacteria, suggesting that they originated from a common ancestor. On the other hand, the enterococcal tufB genes branched with the genera Streptococcus and Lactococcus that form a distinct lineage separated from other low G+C gram-positive bacteria (FIG. 5). The finding that these EF-Tu proteins share some conserved amino acid residues unique to this branch also supports the idea that they may share a common ancestor. Although these conserved residues might result from convergent evolution upon a specialized function, such convergence at the sequence level, even for a few residues, seems to be rare, making it an unlikely event. Moreover, no currently known selective pressure, if any, would account for keeping one versus two tuf genes in bacteria. The G+C contents of enterococcal tufA and tufB sequences are similar, indicating that they both originated from low G+C gram-positive bacteria, in accordance with the phylogenetic analysis.

The tuf genes are present in various copy numbers in different bacteria. Furthermore, the two tuf genes are normally associated with characteristic flanking genes. The two tuf gene copies commonly encountered within gram-negative bacteria are part of the bacterial str operon and tRNA-tufB operon, respectively. The arrangement of tufA in the str operon was also found in a variety of bacteria, including Thermotoga maritima, the most ancient bacteria sequenced so far, Aquifex aeolicus, cyanobacteria, Bacillus sp., Micrococcus luteus, Mycobacterium tuberculosis, and Streptomyces sp. Furthermore, the tRNA-tufB operon has also been identified in Aquifex aeolicus, Thermus thermophilus, and Chlamydia trachomatis. The two widespread tuf gene arrangements argue in favor of their ancient origins. It is noteworthy that most obligate intracellular parasites, such as Mycoplasma sp., R. prowazekii, B. burgdorferi, and T. pallidum, contain only one tuf gene. Their flanking sequences are distinct from the two conserved patterns as a result of selection for effective propagation by an extensive reduction in genome size by intragenomic recombination and rearrangement.

Most gram-positive bacteria with low G+C content sequenced to date contain only a single copy of the tuf gene as a part of the str operon. This is the case for B. subtilis, S. aureus and E. faecalis. PCR amplification using a primer targeting a conserved region of the fus gene and the tufA-specific primer SEQ ID NO. 660, but not the tufB-specific primer SEQ ID NO. 661, yielded the expected amplicons for all 17 enterococcal species tested, indicating the presence of the fus-tuf organization in all enterococci (data not shown). However, in the genomes of S. pneumoniae and S. pyogenes, the sequences flanking the tuf genes varies although the tuf gene itself remains highly conserved. The enterococcal tufB genes are clustered with streptococci, but at present we do not have enough data to identify the genes flanking the enterococcal tufB genes. Furthermore, the functional role of the enterococcal tufB genes remains unknown. One can only postulate that the two divergent gene copies are expressed under different conditions.

The amino acid sequence identities between the enterococcal tufA and tufB genes are lower than either i) those between the enterococcal tufA and the tuf genes from other low G+C gram-positive bacteria (streptococci and lactococci excluded) or ii) those between the enterococcal tufB and streptococcal and lactococcal tuf genes. These findings suggest that the enterococcal tufA genes share a common ancestor with other low G+C gram-positive bacteria via the simple scheme of vertical evolution, while the enterococcal tufB genes are more closely related to those of streptococci and lactococci. The facts that some enterococci possess an additional tuf gene and that the single streptococcal tuf gene is nut clustered with other low G+C gram-positive bacteria cannot be explained by the mechanism of gene duplication or intrachromosomal recombination. According to sequence and phylogenetic analysis, we propose that the presence of the additional copy of the tuf genes in 11 enterococcal species is due to horizontal gene transfer. The common ancestor of the 11 enterococcal species now carrying tufB genes acquired a tuf gene from an ancestral streptococcus or a streptococcus-related species during enterococcal evolution through gene transfer before the diversification of modern enterococci. Further study of the flanking regions of the gene may provide more clues for the origin and function of this gene in enterococci.

Recent studies of genes and genomes have demonstrated that considerable horizontal transfer occurred in the evolution of aminoacyl-tRNA synthetases in all three kingdoms of life. The heterogeneity of 16S rRNA is also attributable to horizontal gene transfer in some bacteria, such as Streptomyces, Thermomonospora chromogena and Mycobacterium celatum. In this study, we provide the first example in support of a likely horizontal transfer of the tuf gene encoding the elongation factor Tu. This may be an exception since stringent functional constraints do not allow for frequent horizontal transfer of the tuf gene as with other genes. However, enterococcal tuf genes should not be the only such exception as we have noticed that the phylogeny of Streptomyces tuf genes is equally or more complex than that of enterococci. For example, the three tuf-like genes in a high G+C gram-positive bacterium, S. ramocissimus, branched with the tuf genes of phylogenetically divergent groups of bacteria (FIG. 5). Another example may be the tuf genes in clostridia, which represent a phylogenetically very broad range of organisms and form a plethora of lines and groups of various complexities and depths. Four species belonging to three different clusters within the genus Clostridium have been shown by Southern hybridization to carry two copies of the tuf gene. Further sequence data and phylogenetic analysis may help interpreting the evolution of the elongation factor Tu in these gram-positive bacteria. Since the tuf genes and 16S rRNA genes are often used for phylogenetic study, the existence of duplicate genes originating from horizontal gene transfer may alter the phylogeny of microorganisms when the laterally acquired copy of the gene is used for such analysis. Hence, caution should be taken in interpreting phylogenetic data. In addition, the two tuf genes in enterococci have evolved separately and are distantly related to each other phylogenetically. The enterococcal tufB genes are less conserved and unique to the 11 enterococcal species only. We previously demonstrated that the enterococcal tufA genes could serve as a target to develop a DNA-based assay for identification of enterococci. The enterococcal tufB genes would also be useful in identification of these 11 enterococcal species.

Example 43 Elongation Factor Tu (tuf) and the F-ATPase Beta-Subunit (atpD) as Phylogenetic Tools for Species of the Family Enterobacteriaceae Summary

The phylogeny of enterobacterial species commonly found in clinical samples was analyzed by comparing partial sequences of their elongation factor Tu (tuf) genes and their F-ATPase beta-subunit (atpD) genes. A 884-bp fragment for tuf and a 884- or 871-bp fragment for atpD were sequenced for 88 strains of 72 species from 25 enterobacterial genera. The atpD sequence analysis revealed a specific indel to Pantoea and Tatumella species showing for the first time a tight phylogenetic affiliation between these two genera. Comprehensive tuf and atpD phylogenetic trees were constructed and are in agreement with each other. Monophyletic genera are Yersinia, Pantoea, Edwardsiella, Cedecea, Salmonella, Serratia, Proteus, and Providencia. Analogous trees were obtained based on available 16S rDNA sequences from databases. tuf and atpD phylogenies are in agreement with the 16S rDNA analysis despite the smaller resolution power for the latter. In fact, distance comparisons revealed that tuf and atpD genes provide a better resolution for pairs of species belonging to the family Enterobacteriaceae. However, 16S rDNA distances are better resolved for pairs of species belonging to different families. In conclusion, tuf and atpD conserved genes are sufficiently divergent to discriminate different species inside the family Enterobacteriaceae and offer potential for the development of diagnostic tests based on DNA to identify enterobacterial species.

Introduction

Members of the family Enterobacteriaceae are facultatively anaerobic gram-negative rods, catalase-positive and oxidase-positive (Brenner, 1984). They are found in soil, water, plants, and in animals from insects to man. Many enterobacteria are opportunistic pathogens. In fact, members of this family are responsible for about 50% of nosocomial infections in the United States (Brenner, 1984). Therefore, this family is of considerable clinical importance.

Major classification studies on the family Enterobacteriaceae are based on phenotypic traits (Brenner et al., 1999; Brenner et al., 1980; Dickey & Zumoff, 1988; Farmer III et al., 1980; Farmer III et al., 1985b; Farmer III et al., 1985a) such as biochemical reactions and physiological characteristics. However, phenotypically distinct strains may be closely related by genotypic criteria and may belong to the same genospecies (Bercovier et al., 1980; Hartl & Dykhuizen, 1984). Also, phenotypically close strains (biogroups) may belong to different genospecies, like Klebsiella pneumoniae and Enterobacter aerogenes (Brenner, 1984) for example. Consequently, identification and classification of certain species may be ambiguous with techniques based on phenotypic tests (Janda et al., 1999; Kitch et al., 1994; Sharma et al., 1990).

More advances in the classification of members of the family Enterobacteriaceae have come from DNA-DNA hybridization studies (Brenner et al., 1993; Brenner et al., 1986; Brenner, et al., 1980; Farmer III, et al., 1980; Farmer III, et al., 1985b; Izard et al., 1981; Steigerwalt et al., 1976). Furthermore, the phylogenetic significance of bacterial classification based on 16S rDNA sequences has been recognized by many workers (Stackebrandt & Goebel, 1994; Wayne et al., 1987). However, members of the family Enterobacteriaceae have not been subjected to extensive phylogenetic analysis of 16S rDNA (Sproer et al., 1999). In fact, this molecule was not thought to solve taxonomic problems concerning closely related species because of its very high degree of conservation (Brenner, 1992; Sproer, et al., 1999). Another drawback of the 16S rDNA gene is that it is found in several copies within the genome (seven in Escherichia coli and Salmonella typhimurium) (Hill & Harnish, 1981). Due to sequence divergence between the gene copies, direct sequencing of PCR products is often not suitable to achieve a representative sequence (Cilia et al., 1996; Hill & Harnish, 1981). Other genes such as gap and ompA (Lawrence et al., 1991), rpoB (Mollet et al., 1997), and infB (Hedegaard et al., 1999) were used to resolve the phylogeny of enterobacteria. However, none of these studies covered an extensive number of species.

tuf and atpD are the genes encoding the elongation factor Tu (EF-Tu) and the F-ATPase beta-subunit, respectively. EF-Tu is involved in peptide chain formation (Ludwig et al., 1990). The two copies of the tuf gene (tufA and tufB) found in enterobacteria (Sela et al., 1989) share high identity level (99%) in Salmonella typhimurium and in E. coli. The recombination phenomenon could explain sequence homogenization between the two copies (Abdulkarim & Hughes, 1996; Grunberg-Manago, 1996). F-ATPase is present on the plasma membranes of eubacteria (Nelson & Taiz, 1989). It functions mainly in ATP synthesis (Nelson & Taiz, 1989) and the beta-subunit contains the catalytic site of the enzyme. EF-Tu and F-ATPase are highly conserved throughout evolution and shows functional constancy (Amann et al., 1988; Ludwig, et al., 1990). Recently, phylogenies based on protein sequences from EF-Tu and F-ATPase beta-subunit showed good agreement with each other and with the rDNA data (Ludwig et al., 1993).

We elected to sequence 884-bp fragments of tuf and atpD from 88 clinically relevant enterobacterial strains representing 72 species from 25 genera. These sequences were used to create phylogenetic trees that were compared with 16S rDNA trees. These trees revealed good agreement with each others and demonstrated the high resolution of tuf and atpD phylogenies at the species level.

Materials and Methods

Bacterial strains and genomic material. All bacterial strains used in this study were obtained from the American Type Culture Collection (ATCC) or the Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH (DSMZ). These enterobacteria can all be recovered from clinical specimens, but not all are pathogens. Whenever possible, we choose type strains. Identification of all strains was confirmed by classical biochemical tests using the automated system MicroScan WalkAway-96 system equipped with a Negative BP Combo Panel Type 15 (Dade Behring Canada). Genomic DNA was purified using the G NOME DNA kit (Bio 101). Genomic DNA from Yersinia pestis was kindly provided by Dr. Robert R. Brubaker. Strains used in this study and their descriptions are shown in Table 19.

PCR primers. The eubacterial tuf and atpD gene sequences available from public databases were analyzed using the GCG package (version 8.0) (Genetics Computer Group). Based on multiple sequence alignments, two highly conserved regions were chosen for each genes, and PCR primers were derived from these regions with the help of Oligo primer analysis software (version 5.0) (National Biosciences). A second 5′ primer was design to amplify the gene atpD for few enterobacteria difficult to amplify with the first primer set. When required, the primers contained inosines or degeneracies to account for variable positions. Oligonucleotide primers were synthesized with a model 394 DNA/RNA synthesizer (PE Applied Biosystems). PCR primers used in this study are listed in Table 20.

DNA sequencing. An 884-bp portion of the tuf gene and an 884-bp portion (or alternatively an 871-bp portion for a few enterobacterial strains) of the atpD gene were sequenced for all enterobacteria listed in the first strain column of Table 19. Amplification was performed with 4 ng of genomic DNA. The 40-μl PCR mixtures used to generate PCR products for sequencing contained 1.0 μM each primer, 200 μM each deoxyribonucleoside triphosphate (Pharmacia Biotech), 10 mM Tris-HCl (pH 9.0 at 25° C.), 50 mM KCl, 0.1% (w/v) Triton X-100, 2.5 mM MgCl₂, 0.05 mM BSA, 0.3 U of Taq DNA polymerase (Promega) coupled with TaqStart™ antibody (Clontech Laboratories). The TaqStart™ neutralizing monoclonal antibody for Taq DNA polymerase was added to all PCR mixtures to enhance efficiency of amplification (Kellogg et al., 1994). The PCR mixtures were subjected to thermal cycling (3 min at 95° C. and then 35 cycles of 1 min at 95° C., 1 min at 55° C. for tuf or 50° C. for atpD, and 1 min at 72° C., with a 7-min final extension at 72° C.) using a PTC-200 DNA Engine thermocycler (MJ Research). PCR products having the predicted sizes were recovered from an agarose gel stained for 15 min with 0.02% of methylene blue followed by washing in sterile distilled water for 15 min twice (Flores et al., 1992). Subsequently, PCR products having the predicted sizes were recovered from gels using the QIAquick gel extraction kit (QIAGEN).

Both strands of the purified amplicons were sequenced using the ABI Prism BigDye Terminator Cycle Sequencing Ready Reaction Kit (PE Applied Biosystems) on an automated DNA sequencer (Model 377). Amplicons from two independent PCR amplifications sequenced for each strain to ensure the absence of sequencing errors attributable to nucleotide miscorporations by the Taq DNA polymerase. Sequence assembly was performed with the aid of Sequencher 3.0 software (Gene Codes).

Phylogenetic analysis. Multiple sequence alignments were performed using PileUp from the GCG package (Version 10.0) (Genetics Computer Group) and checked by eye with the editor SeqLab to edit sequences if necessary and to note which regions were to be excluded for phylogenetic analysis. Vibrio cholerae and Shewanella putrefaciens were used as outgroups. Bootstrap subsets (750 sets) and phylogenetic trees were generated with the Neighbor Joining algorithm from Dr. David Swofford's PAUP (Phylogenetic Analysis Using Parsimony) Software version 4.0b4 (Sinauer Associates) and with tree-bisection branch-swapping. The distance model used was Kimura (1980) two-parameter. Relative rate test was performed with the aid of Phyltest program version 2.0 (c).

Results and Discussion DNA Amplification, Sequencing And Sequence Alignments

A PCR product of the expected size of 884 by was obtained for tuf and of 884 or 871 by for atpD from all bacterial strains tested. After subtracting for biased primer regions and ambiguous single strand data, sequences of at least 721 by for tuf and 713 by for atpD were submitted to phylogenetic analyses. These sequences were aligned with tuf and atpD sequences available in databases to verify that the nucleotide sequences indeed encoded a part of tested genes. Gaps were excluded to perform phylogenetic analysis.

Signature Sequences

From the sequence alignments obtained from both tested genes, only one insertion was observed. This five amino acids insertion is located between the positions 325 and 326 of atpD gene of E. coli strain K-12 (Saraste et al., 1981) and can be considered a signature sequence of Tatumella ptyseos and Pantoea species (FIG. 7). The presence of a conserved indel of defined length and sequence and flanked by conserved regions could suggest a common ancestor, particularly when members of a given taxa share this indel (Gupta, 1998). To our knowledge, high relatedness between the genera Tatumella and Pantoea is demonstrated for the first time.

Enterobacter agglomerans ATCC 27989 sequence does not possess the five amino acid indel (FIG. 7). This indel could represent a useful marker to help resolve the Enterobacter agglomerans and Pantoea classification. Indeed, the transfer of Enterobacter agglomerans to Pantoea agglomerans was proposed in 1989 by Gavini et al. (Gavini et al., 1989). However, some strains are provisionally classified as Pantoea sp. until their interrelatedness is elucidated (Gavini, et al., 1989). Since the transfer was proposed, the change of nomenclature has not yet been made for all Enterobacter agglomerans in the ATCC database. The absence of the five amino acids indel suggests that some strains of Enterobacter agglomerans most likely do not belong to the genus Pantoea.

Phylogenetic Trees Based on Partial Tuf Sequences, Atpd Sequences, and Published 16S Rdna Data of Members of the Enterobacteriaceae.

Representative trees constructed from tuf and atpD sequences with the neighbor-joining method are shown in FIG. 8. The phylogenetic trees generated from partial tuf sequences and atpD sequences are very similar. Nevertheless, atpD tree shows more monophyletic groups corresponding to species that belong to the same genus. These groups are more consistent with the actual taxonomy. For both genes, some genera are not monophyletic. These results support previous phylogenies based on the genes gap and ompA (Lawrence, et al., 1991), rpoB (Mollet, et al., 1997), and infB (Hedegaard, et al., 1999) which all showed that the genera Escherichia and Klebsiella are polyphyletic. There were few differences in branching between tuf and atpD genes.

Even though Pantoea agglomerans and Pantoea dispersa indels were excluded for phylogenetic analysis, these two species grouped together and were distant from Enterobacter agglomerans ATCC 27989, adding another evidence that the latter species is heterogenous and that not all members of this species belong to the genus Pantoea. In fact, the E. agglomerans strain ATCC 27989 exhibits branch lengths similar to others Enterobacter species with both genes. Therefore, we suggest that this strain belong to the genus Enterobacter until further reclassification of that genus.

tuf and atpD trees exhibit very short genetic distances between taxa belonging to the same genetic species including species segregated for clinical considerations. This first concern E. coli and Shigella species that were confirmed to be the same genetic species by hybridization studies (Brenner et al., 1972; Brenner et al., 1972; Brenner et al., 1982) and phylogenies based on 16S rDNA (Wang et al., 1997) and rpoB genes (Mollet, et al., 1997). Hybridization studies (Bercovier, et al., 1980) and phylogeny based on 16S rDNA genes (Ibrahim et al., 1994) demonstrated also that Yersinia pestis and Y. pseudotuberculosis are the same genetic species. Among Yersinia pestis and Y. pseudotuberculosis, the three Klebsiella pneumoniae subspecies, E. coli-Shigella species, and Salmonella choleraesuis subspecies, Salmonella is a less tightly knit species than the other genetic species. The same is true for E. coli and Shigella species.

Escherichia fergusonii is very close to E. coli-Shigella genetic species. This observation is corroborated by 16S rDNA phylogeny (McLaughlin et al., 2000) but not by DNA hybridization values. In fact, E. fergusonii is only 49% to 63% related to E. coli-Shigella (Farmer III, et al., 1985b). It was previously observed that very recently diverged species may not be recognizable based on 16S rDNA sequences although DNA hybridization established them as different species (Fox et al., 1992). Therefore, E. fergusonii could be a new “quasi-species”.

atpD phylogeny revealed Salmonella subspecies divisions consistent with the actual taxonomy. This result was already observed by Christensen et al. (Christensen & Olsen, 1998). Nevertheless, tuf partial sequences discriminate less than atpD between Salmonella subspecies.

Overall, tuf and atpD phylogenies exhibit enough divergence between species to ensure efficient discrimination. Therefore, it could be easy to distinguish phenotypically close enterobacteria belonging to different genetic species such as Klebsiella pneumoniae and Enterobacter aerogenes.

Phylogenetic relationships between Salmonella, E. coli and C. freundii are not well defined. 16S rDNA and 23S rDNA sequence data reveals a closer relationship between Salmonella and E. coli than between Salmonella and C. freundii (Christensen et al., 1998), while DNA homology studies (Selander et al., 1996) and infB phylogeny (Hedegaard, et al., 1999) showed that Salmonella is more closely related to C. freundii than to E. coli. In that regard, tuf and atpD phylogenies are coherent with 16S rDNA and 23S rDNA sequence analysis.

Phylogenetic analyses were also performed using amino acids sequences. tuf tree based on amino acids is characterized by a better resolution between taxa outgroup and taxa ingroup (enterobacteria) than tree based on nucleic acids whereas atpD trees based on amino acids and nucleic acids give almost the same resolution between taxa outgroup and ingroup (data not shown).

Relative rate test (or two cluster test (Takezaki et al., 1995)) evaluates if evolution is constant between two taxa. Before to apply the test, the topology of a tree is determined by tree-building method without the assumption of rate constancy. Therefore, two taxa (or two groups of taxa) are compared with a third taxon that is an outgroup of the first two taxa (Takezaki, et al., 1995). Few pairs of taxa that exhibited a great difference between their branch lengths at particular nodes were chosen to perform the test. This test reveals that tuf and atpD are not constant in their evolution within the family Enterobacteriaceae. For tuf, for example, the hypothesis of rate constancy is rejected (Z value higher than 1.96) between Yersinia species. The same is true for Proteus species. For atpD, for example, evolution is not constant between Proteus species, between Proteus species and Providencia species, and between Yersinia species and Escherichia coli. For 16S rDNA, for example, evolution is not constant between two E. coli, between E. coli and Enterobacter aerogenes, and between E. coli and Proteus vulgaris. These results suggest that tuf, atpD and 16S rDNA could not serve as a molecular clock for the entire family Enterobacteriaceae.

Since the number and the nature of taxa can influence topology of trees, phylogenetic trees from tuf and atpD were reconstructed using sequences corresponding to strains for which 16S rDNA genes were published in GenEMBL. These trees were similar to those generated using 16S rDNA (FIG. 9). Nevertheless, 16S rDNA tree gave poorer resolution power than tuf and atpD gene trees. Indeed, these latter exhibited less multifurcation (polytomy) than the 16S rDNA tree.

Comparison of Distances Based on tuf, atpD, and 16S rDNA data.

tuf, atpD, and 16S rDNA distances (i.e. the number of differences per nucleotide site) were compared with each other for each pair of strains. We found that the tuf and atpD distances were respectively 2.268±0.965 and 2.927±0.896 times larger than 16S rDNA distances (FIGS. 10 a and b). atpD distances were 1.445±0.570 times larger than tuf distances (FIG. 10 c). FIG. 10 also shows that the tuf, atpD, and 16S rDNA distances between members of different species of the same genus (0.053±0.034, 0.060±0.020, and 0.024±0.010, respectively) were in mean smaller than the distances between members of different genera belonging to the same family (0.103±0.053, 0.129±0.051, and 0.044±0.013, respectively). However, the overlap exhibits with standard deviations add to a focus of evidences that some enterobacterial genera are not well defined (Brenner, 1984). In fact, many distances for pairs of species especially belonging to the genera Escherichia, Shigella, Enterobacter, Citrobacter, Klebsiella, and Kluyvera overlap distances for pairs of species belonging to the same genus (FIG. 10). For example, distances for pairs composed by species of Citrobacter and species of Klebsiella overlap distances for pairs composed by two Citrobacter or by two Klebsiella.

Observing the distance distributions, 16S rDNA distances reveal a clear separation between the families Enterobacteriaceae and Vibrionaceae despite the fact that the family Vibrionaceae is genetically very close to the Enterobacteriaceae (FIGS. 10 a and b). Nevertheless, tuf and atpD show higher discriminating power below the family level (FIGS. 10 a and b).

There were some discrepancies in the relative distances for the same pairs of taxa between the two genes studied. First, distances between Yersinia species are at least two times lower for atpD than for tuf (FIG. 10 c). Also, distances at the family level (between Enterobacteriaceae and Vibrionaceae) show that Enterobacteriaceae is a tightlier knit family with atpD gene (Proteus genus excepted) than with tuf gene. Both genes well delineate taxa belonging to the same species. There is one exception with atpD: Klebsiella planticola and K. ornithinolithica belong to the same genus but fit with taxa belonging to the same species (FIGS. 10 a and c). These two species are also very close genotypically with tuf gene. This suggest that Klebsiella planticola and K. ornithinolithica could be two newborn species. tuf and atpD genes exhibit little distances between Escherichia fergusonii and E. coli-Shigella species. Unfortunately, comparison with 16S rDNA could not be achieved because the E. fergusonii 16S rDNA sequence is not yet accessible in GenEMBL database. Therefore, the majority of phenotypically close enterobacteria could be easily discriminated genotypically using tuf and atpD gene sequences.

In conclusion, tuf and atpD genes exhibit phylogenies consistent with 16S rDNA genes phylogeny. For example, they reveal that the family Enterobacteriaceae is monophyletic. Moreover, tuf and atpD distances provide a higher discriminating power than 16S rDNA distances. In fact, tuf and atpD genes discriminate well between different genospecies and are conserved between strains of the same genetic species in such a way that primers and molecular probes for diagnostic purposes could be designed. Preliminary studies support these observations and diagnostic tests based on tuf and atpD sequence data to identify enterobacteria are currently under development.

Example 44 Testing New Pairs of PCR Primers Selected from Two Species-Specific Genomic DNA Fragments which are Objects of Our Assigned U.S. Pat. No. 6,001,564

Objective. The goal of these experiments is to demonstrate that it is relatively easy for a person skilled in the art to find other PCR primer pairs from the species-specific fragments used as targets for detection and identification of a variety of microorganisms. In fact, we wish to prove that the PCR primers previously tested by our group and which are objects of the present patent application are not the only possible good choices for diagnostic purposes. For this example, we used diagnostic targets described in our assigned U.S. Pat. No. 6,001,564.

Experimental strategy. We have selected randomly two species-specific genomic DNA fragments for this experiment. The first one is the 705-bp fragment specific to Staphylococcus epidermidis (SEQ ID NO: 36 from U.S. Pat. No. 6,001,564) while the second one is the 466-bp fragment specific to Moraxella catarrhalis (SEQ ID NO: 29 from U.S. Pat. No. 6,001,564). Subsequently, we have selected from these two fragments a number of PCR primer pairs other than those previously tested. We have chosen 5 new primer pairs from each of these two sequences which are well dispersed along the DNA fragment (FIGS. 11 and 12). We have tested these primers for their specificity and compared them with the original primers previously tested. For the specificity tests, we have tested all bacterial species closely related to the target species based on phylogenetic analysis with three conserved genes (rRNA genes, tuf and atpD). The rational for selecting a restricted number of bacterial species to evaluate the specificity of the new primer pairs is based on the fact that the lack of specificity of a DNA-based assay is attributable to the detection of closely related species which are more similar at the nucleotide level. Based on the phylogenetic analysis, we have selected (i) species from the closely related genus Staphylococcus, Enterococcus, Streptococcus and Listeria to test the specificity of the S. epidermidis-specific PCR assays and (ii) species from the closely related genus Moraxella, Kingella and Neisseria to test the specificity of the M. catarrhalis-specific PCR assays.

Materials and Methods

Bacterial strains. All bacterial strains used for these experiments were obtained from the American Type Culture Collection (ATCC, Rockville, Md.).

Genomic DNA isolation. Genomic DNA was purified from the ATCC reference strains by using the G-nome DNA kit (Bio 101 Inc., Vista, Calif.).

Oligonucleotide design and synthesis. PCR primers were designed with the help of the Oligo™ primer analysis software Version 4.0 (National Biosciences Inc., Plymouth, Minn.) and synthesized using a model 391 DNA synthesizer (Applied Biosystems, Foster City, Calif.).

PCR assays. All PCR assays were performed by using genomic DNA purified from reference strains obtained from the ATCC. One μl of purified DNA preparation (containing 0.01 to 1 ng of DNA per μl) was added directly into the PCR reaction mixture. The 20 μL PCR reactions contained final concentrations of 50 mM KCl, 10 mM Tris-HCl (pH 9.0), 0.1% Triton X-100, 2.5 mM MgCl₂, 0.4 μM of each primer, 200 μM of each of the four dNTPs and 0.5 unit of Taq DNA polymerase (Promega, Madison, Wis.) combined with the TaqStart™ antibody (Clontech Laboratories Inc., Palo Alto, Calif.). An internal control was integrated into all amplification reactions to verify the efficiency of the amplification reaction as well as to ensure that significant PCR inhibition was absent. Primers amplifying a region of 252 by from a control plasmid added to each amplification reaction were used to provide the internal control. PCR reactions were then subjected to thermal cycling (3 min at 95° C. followed by 30 cycles of 1 second at 95° C. for the denaturation step and 30 seconds at 50 to 65° C. for the annealing-extension step) using a PTC-200 thermal cycler (MJ Research Inc., Watertown, Mass.). PCR amplification products were then analyzed by standard agarose gel (2%) electrophoresis. Amplification products were visualized in agarose gels containing 0.25 μg/mL of ethidium bromide under UV at 254 nm.

Results

Tables 21 and 22 show the results of specificity tests with the 5 new primer pairs selected from SEQ ID NO: 29 (specific to M. catarrhalis from U.S. Pat. No. 6,001,564) and SEQ ID NO: 36 (specific to S. epidermidis from U.S. Pat. No. 6,001,564), respectively. In order to evaluate the performance of these new primers pairs, we compared them in parallel with the original primer pairs previously tested.

For M. catarrhalis, all of the 5 selected PCR primer pairs were specific for the target species because none of the closely related species could be amplified (Table 21). In fact, the comparison with the original primer pair SEQ ID NO: 118+SEQ ID NO: 119 (from U.S. Pat. No. 6,001,564) revealed that all new pairs showed identical results in terms of specificity and sensitivity thereby suggesting their suitability for diagnostic purposes.

For S. epidermidis, 4 of the 5 selected PCR primer pairs were specific for the target species (Table 22). It should be noted that for 3 of these four primer pairs the annealing temperature had to be increased from 55° C. to 60 or 65° C. to attain specificity for S. epidermidis. Again the comparison with the original primer pair SEQ ID NO: 145+SEQ ID NO: 146 (from U.S. Pat. No. 6,001,564) revealed that these four primer pairs were as good as the original pair. Increasing the annealing temperature for the PCR amplification is well known by persons skilled in the art to be a very effective way to improve the specificity of a PCR assay (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.; Ehrlich and Greenberg, 1994, PCR-based Diagnostics in Infectious Disease, Blackwell Scientific Publications, Boston, Mass.). In fact, those skilled in the art are well aware of the fact that the annealing temperature is critical for the optimization of PCR assays. Only the primer pair VBsep3+VBsep4 amplified bacterial species other than S. epidermidis including the staphylococcal species S. capitis, S. cohnii, S. aureus, S. haemolyticus and S. hominis (Table 22). For this non-specific primer pair, increasing the annealing temperature from 55 to 65° C. was not sufficient to attain the desired specificity. One possible explanation for the fact that it appears slightly easier to select species-specific primers for M catarrhalis than for S. epidermidis is that M catarrhalis is more isolated in phylogenetic trees than S. epidermidis. The large number of coagulase negative staphylococcal species such as S. epidermidis is largely responsible for this phylogenetic clustering.

Conclusion

These experiment clearly show that it is relatively easy for a person skilled in the art to select, from the species-specific DNA fragments selected as target for identification, PCR primer pairs suitable for diagnostic purposes other than those previously tested. The amplification conditions can be optimize by modifying critical variables such as the annealing temperature to attain the desired specificity and sensitivity. Consequently, we consider that it is legitimate to claim any possible primer sequences selected from the species-specific fragment and that it would be unfair to grant only the claims dealing with the primer pairs previously tested. By extrapolation, these results strongly suggest that it is also relatively easy for a person skilled in the art to select, from the species-specific DNA fragments, DNA probes suitable for diagnostic purposes other than those previously tested.

Example 45 Testing Modified Versions of PCR Primers Derived from the Sequence of Several Primers which are Objects of U.S. Pat. No. 6,001,564.

Objective. The purpose of this project is to verify the efficiency of amplification by modified PCR primers derived from primers previously tested. The types of primer modifications to be tested include (i) variation of the sequence at one or more nucleotide positions and (ii) increasing or reducing the length of the primers. For this example, we used diagnostic targets described in U.S. Pat. No. 6,001,564.

Experimental Strategy:

Testing Primers with Nucleotide Changes

We have designed 13 new primers which are derived from the S. epidermidis-specific SEQ ID NO: 146 from U.S. Pat. No. 6,001,564 (Table 23). These primers have been modified at one or more nucleotide positions. As shown in Table 23, the nucleotide changes were introduced all along the primer sequence. Furthermore, instead of modifying the primer at any nucleotide position, the nucleotide changes were introduced at the third position of each codon to better reflect potential genetic variations in vivo. It should be noted that no nucleotide changes were introduced at the 3′ end of the oligonucleotide primers because those skilled in the art are well aware of the fact that mismatches at the 3′ end should be avoided (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). All of these modified primers were tested in PCR assays in combination with SEQ ID NO: 145 from U.S. Pat. No. 6,001,564 and the efficiency of the amplification was compared with the original primer pair SEQ ID NO: 145+SEQ ID NO: 146 previously tested in U.S. Pat. No. 6,001,564.

Testing Shorter or Longer Versions of Primers

We have designed shorter and longer versions of the original S. epidermidis-specific PCR primer pair SEQ ID NO: 145+146 from U.S. Pat. No. 6,001,564 (Table 24) as well as shorter versions of the original P. aeruginosa-specific primer pair SEQ ID NO: 83+84 from U.S. Pat. No. 6,001,564 (Table 25). As shown in Tables 24 and 25, both primers of each pair were shortened or lengthen to the same length. Again, those skilled in the art know that the melting temperature of both primers from a pair should be similar to avoid preferential binding at one primer binding site which is detrimental in PCR (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.; Ehrlich and Greenberg, 1994, PCR-based Diagnostics in Infectious Disease, Blackwell Scientific Publications, Boston, Mass.). All of these shorter or longer primer versions were tested in PCR assays and the efficiency of the amplification was compared with the original primer pair SEQ ID NOs 145 and 146.

Materials and Methods

See the Materials and methods section of Example 44.

Results

Testing Primers with Nucleotide Changes

The results of the PCR assays with the 13 modified versions of SEQ ID NO: 146 from U.S. Pat. No. 6,001,564 are shown in Table 23. The 8 modified primers having a single nucleotide variation showed an efficiency of amplification identical to the original primer pair based on testing with 3 different dilutions of genomic DNA. The four primers having two nucleotide variations and primer VBmut12 having 3 nucleotide changes also showed PCR results identical to those obtained with the original pair. Finally, primer VBmut13 with four nucleotide changes showed a reduction in sensitivity by approximately one log as compared with the original primer pair. However, reducing the annealing temperature from 55 to 50° C. gave an efficiency of amplification very similar to that observed with the original primer pair (Table 23). In fact, reducing the annealing temperature of PCR cycles represents an effective way to reduce the stringency of hybridization for the primers and consequently allows the binding of probes with mismatches (Persing et al., 1993, Diagnostic Molecular Microbiology: Principles and Applications, American Society for Microbiology, Washington, D.C.). Subsequently, we have confirmed the specificity of the PCR assays with each of these 13 modified versions of SEQ ID NO: 146 from U.S. Pat. No. 6,001,564 by performing amplifications from all bacterial species closely related to S. epidermidis which are listed in Table 22.

Testing Shorter or Longer Versions of Primers

For these experiments, two primer pairs were selected: i) SEQ ID NO: 145+146 from U.S. Pat. No. 6,001,564 (specific to S. epidermidis) which are AT rich and ii) SEQ ID NO: 83+84 (specific to P. aeruginosa) which are GC rich. For the AT rich sequence, primers of 15 to 30 nucleotide in length were designed (Table 24) while for the GC rich sequences, primers of 13 to 19 nucleotide in length were designed (Table 25).

Table 24 shows that, for an annealing temperature of 55° C., the 30-25-, 20- and 17-nucleotide versions of SEQ ID NO: 145 and 146 from U.S. Pat. No. 6,001,564 all showed identical results as compared with the original primer pair except that the 17-nucleotide version amplified slightly less efficiently the S. epidermidis DNA. Reducing the annealing temperature from 55 to 45° C. for the 17-nucleotide version allowed to increase the amplification efficiency to a level very similar to that with the original primer pair (SEQ ID NO: 145+146 from U.S. Pat. No. 6,001,564). Regarding the 15-nucleotide version, there was amplification of S. epidermidis DNA only when the annealing temperature was reduced to 45° C. Under those PCR conditions the assay remained S. epidermidis-specific but the amplification signal with S. epidermidis DNA was slightly lower as compared with the original primer pair. Subsequently, we have further confirmed the specificity of the shorter or longer versions by amplifying DNA from all bacterial species closely related to S. epidermidis which are listed in Table 22.

Table 25 shows that, for an annealing temperature of 55° C., all shorter versions of SEQ ID NO: 83 and 84 from U.S. Pat. No. 6,001,564 showed identical PCR results as compared with the original primer pair. As expected, these results show that it is simpler to reduce the length of GC rich as compared with AT rich. This is attributable to the fact that GC binding is more stable than AT binding.

Conclusion

Testing Primers with Nucleotide Changes

The above experiments clearly show that PCR primers may be modified at one or more nucleotide positions without affecting the specificity and the sensitivity of the PCR assay. These results strongly suggest that a given oligonucleotide can detect variant genomic sequences from the target species. In fact, the nucleotide changes in the selected primers were purposely introduced at the third position of each codon to mimic nucleotide variation in genomic DNA. Thus we conclude that it is justified to claim “a variant thereof” for i) the SEQ IDs of the fragments and oligonucleotides which are object of the present patent application and ii) genomic variants of the target species.

Testing Shorter or Longer Versions of Primers

The above experiments clearly show that PCR primers may be shorter or longer without affecting the specificity and the sensitivity of the PCR assay. We have showed that oligonucleotides ranging in sizes from 13 to 30 nucleotides may be as specific and sensitive as the original primer pair from which they were derived. Consequently, these results suggest that it is not exaggerated to claim sequences having at least 12 nucleotide in length.

This invention has been described herein above, and it is readily apparent that modifications can be made thereto without departing from the spirit of this invention. These modifications are under the scope of this invention, as defined in the appended claims.

TABLE 1 Distribution (%) of nosocomial pathogens for various human infections in USA (1990-1992)¹. Pathogen UTI² SSI³ BSI⁴ Pneumonia CSF⁵ Escherichia coli 27 9 5 4 2 Staphylococcus aureus 2 21 17 21 2 Staphylococcus epidermidis 2 6 20 0 1 Enterococcus faecalis 16 12 9 2 0 Enterococcus faecium 1 1 0 0 0 Pseudomonas aeruginosa 12 9 3 18 0 Klebsiella pneumoniae 7 3 4 9 0 Proteus mirabilis 5 3 1 2 0 Streptococcus pneumoniae 0 0 3 1 18 Group B Streptococci 1 1 2 1 6 Other streptococci 3 5 2 1 3 Haemophilus influenzae 0 0 0 6 45 Neisseria meningitidis 0 0 0 0 14 Listeria monocytogenes 0 0 0 0 3 Other enterococci 1 1 0 0 0 Other staphylococci 2 8 13 2 0 Candida albicans 9 3 5 5 0 Other Candida 2 1 3 1 0 Enterobacter sp. 5 7 4 12 2 Acinetobacter sp. 1 1 2 4 2 Citrobacter sp. 2 1 1 1 0 Serratia marcescens 1 1 1 3 1 Other Klebsiella 1 1 1 2 1 Others 0 6 4 5 0 ¹Data recorded by the National Nosocomial Infections Surveillance (NNIS) from 80 hospitals (Emori and Gaynes, 1993, Clin. Microbiol. Rev., 6: 428-442). ²Urinary tract infection. ³Surgical site infection. ⁴Bloodstream infection. ⁵Cerebrospinal fluid.

TABLE 2 Distribution (%) of bloodstream infection pathogens in Quebec (1995), Canada (1992), UK (1969-1988) and USA (1990-1992). UK³ Community- Hospital- USA⁴ Organism Quebec¹ Canada² acquired acquired Hospital-acquired E. coli 15.6 53.8 24.8 20.3 5.0 S. epidermidis and 25.8 — 0.5 7.2 31.0 other CoNS⁵ S. aureus 9.6 — 9.7 19.4 16.0 S. pneumoniae 6.3 — 22.5 2.2 — E. faecalis 3.0 — 1.0 4.2 — E. faecium 2.6 — 0.2 0.5 — Enterococcus sp. — — — — 9.0 H. influenzae 1.5 — 3.4 0.4 — P. aeruginosa 1.5 8.2 1.0 8.2 3.0 K. pneumoniae 3.0 11.2 3.0 9.2 4.0 P. mirabilis — 3.9 2.8 5.3 1.0 S. pyogenes — — 1.9 0.9 — Enterobacter sp. 4.1 5.5 0.5 2.3 4.0 Candida sp. 8.5 — — 1.0 8.0 Others 18.5 17.4 28.7 18.9 19.0 ¹Data obtained for 270 isolates collected at the Centre Hospitalier del'Université Laval (CHUL) during a 5 month period (May to October 1995). ²Data from 10 hospitals throughout Canada representing 941 gram-negative isolates. (Chamberland et al., 1992, Clin. Infect. Dis., 15: 615-628). ³Data from a 20-year study (1969-1988) for nearly 4000 isolates. (Eykyn et al., 1990, J. Antimicrob. Chemother., Suppl. C, 25: 41-58). ⁴Data recorded by the National Nosocomial Infections Surveillance (NNIS) from 80 hospitals (Emori and Gaynes, 1993, Clin. Microbiol. Rev., 6: 428-442). ⁵Coagulase-negative staphylococci.

TABLE 3 Distribution of positive and negative clinical specimens tested at the microbiology laboratory of the CHUL (February 1994-January 1995). % Clinical specimens No. of samples % of positive of negative and/or sites tested (%) specimens specimens Urine 17,981 (54.5)   19.4 80.6 Blood culture/marrow 10,010 (30.4)   6.9 93.1 Sputum 1,266 (3.8)   68.4 31.6 Superficial pus 1,136 (3.5)   72.3 27.7 Cerebrospinal fluid 553 (1.7) 1.0 99.0 Synovial fluid 523 (1.6) 2.7 97.3 Respiratory tract 502 (1.5) 56.6 43.4 Deep pus 473 (1.4) 56.8 43.2 Ears 289 (0.9) 47.1 52.9 Pleural and pericardial fluid 132 (0.4) 1.0 99.0 Peritoneal fluid 101 (0.3) 28.6 71.4 Total: 32,966 (100.0)  20.0 80.0

TABLE 4 Example of microbial species for which tuf and/or atpD and/or recA nucleic acids and/or sequences are used in the present invention. Bacterial species Abiotrophia adiacens Abiotrophia defectiva Achromobacter xylosoxidans subsp. denitrificans Acetobacterium woodi Acetobacter aceti Acetobacter altoacetigenes Acetobacter polyoxogenes Acholeplasma laidlawii Acidothermus cellulolyticus Acidiphilum facilis Acinetobacter baumannii Acinetobacter calcoaceticus Acinetobacter lwoffii Actinomyces meyeri Aerococcus viridans Aeromonas hydrophila Aeromonas salmonicida Agrobacterium radiobacter Agrobacterium tumefaciens Alcaligenes faecalis subsp. faecalis Allochromatium vinosum Anabaena variabilis Anacystis nidulans Anaerorhabdus furcosus Aquifex aeolicus Aquifex pyrophilus Arcanobacterium haemolyticum Archaeoglobus fulgidus Azotobacter vinelandii Bacillus anthracis Bacillus cereus Bacillus firmus Bacillus halodurans Bacillus megaterium Bacillus mycoides Bacillus pseudomycoides Bacillus stearothermophilus Bacillus subtilis Bacillus thuringiensis Bacillus weihenstephanensis Bacteroides distasonis Bacteroides fragilis Bacteroides forsythus Bacteroides ovatus Bacteroides vulgatus Bartonella henselae Bifidobacterium adolescentis Bifidobacterium breve Bifidobacterium dentium Bifidobacterium longum Blastochloris viridis Borrelia burgdorferi Bordetella pertussis Bordetella bronchiseptica Brucella abortus Brevibacterium linens Brevibacterium flavum Brevundimonas diminuta Buchnera aphidicola Budvicia aquatica Burkholderia cepacia Burkholderia mallei Burkholderia pseudomallei Buttiauxella agrestis Butyrivibrio fibrisolvens Campylobacter coli Campylobacter curvus Campylobacter fetus subsp. fetus Campylobacter fetus subsp. venerealis Campylobacter gracilis Campylobacter jejuni Campylobacter jejuni subsp. doylei Campylobacter jejuni subsp. jejuni Campylobacter lari Campylobacter rectus Campylobacter sputorum subsp. sputorum Campylobacter upsaliensis Cedecea davisae Cedecea lapagei Cedecea neteri Chlamydia pneumoniae Chlamydia psittaci Chlamydia trachomatis Chlorobium vibrioforme Chloroflexus aurantiacus Chryseobacterium meningosepticum Citrobacter amalonaticus Citrobacter braakii Citrobacter farmeri Citrobacter freundii Citrobacter koseri Citrobacter sedlakii Citrobacter werkmanii Citrobacter youngae Clostridium acetobutylicum Clostridium beijerinckii Clostridium bifermentans Clostridium botulinum Clostridium difficile Clostridium innocuum Clostridium histolyticum Clostridium novyi Clostridium septicum Clostridium perfringens Clostridium ramosum Clostridium tertium Clostridium tetani Comamonas acidovorans Corynebacterium accolens Corynebacterium bovis Corynebacterium cervicis Corynebacterium diphtheriae Corynebacterium flavescens Corynebacterium genitalium Corynebacterium glutamicum Corynebacterium jeikeium Corynebacterium kutscheri Corynebacterium minutissimum Corynebacterium mycetoides Corynebacterium pseudodiphtheriticum Corynebacterium pseudogenitalium Corynebacterium pseudotuberculosis Corynebacterium renale Corynebacterium striatum Corynebacterium ulcerans Corynebacterium urealyticum Corynebacterium xerosis Coxiella burnetii Cytophaga lytica Deinococcus radiodurans Deinonema sp. Edwardsiella hoshinae Edwardsiella tarda Ehrlichia canis Ehrlichia risticii Eikenella corrodens Enterobacter aerogenes Enterobacter agglomerans Enterobacter amnigenus Enterobacter asburiae Enterobacter cancerogenus Enterobacter cloacae Enterobacter gergoviae Enterobacter hormaechei Enterobacter sakazakii Enterococcus avium Enterococcus casseliflavus Enterococcus cecorum Enterococcus columbae Enterococcus dispar Enterococcus durans Enterococcus faecalis Enterococcus faecium Enterococcus flavescens Enterococcus gallinarum Enterococcus hirae Enterococcus malodoratus Enterococcus mundtii Enterococcus pseudoavium Enterococcus raffinosus Enterococcus saccharolyticus Enterococcus solitarius Enterococcus sulfureus Clostridium sordellii Erwinia amylovora Erwinia carotovora Escherichia coli Escherichia fergusonii Escherichia hermannii Escherichia vulneris Eubacterium lentum Eubacterium nodatum Ewingella americana Francisella tularensis Frankia alni Fervidobacterium islandicum Fibrobacter succinogenes Flavobacterium ferrigeneum Flexistipes sinusarabici Fusobacterium gonidiaformans Fusobacterium necrophorum subsp. necrophorum Fusobacterium nucleatum subsp. polymorphum Gardnerella vaginalis Gemella haemolysans Gemella morbillorum Globicatella sanguis Gloeobacter violaceus Gloeothece sp. Gluconobacter oxydans Haemophilus actinomycetemcomitans Haemophilus aphrophilus Haemophilus ducreyi Haemophilus haemolyticus Haemophilus influenzae Haemophilus parahaemolyticus Haemophilus parainfluenzae Haemophilus paraphrophilus Haemophilus segnis Hafnia alvei Halobacterium marismortui Halobacterium salinarum Haloferax volcanii Helicobacter pylori Herpetoshiphon aurantiacus Kingella kingae Klebsiella ornithinolytica Klebsiella oxytoca Klebsiella planticola Klebsiella pneumoniae subsp. ozaenae Klebsiella pneumoniae subsp. pneumoniae Klebsiella pneumoniae subsp. rhinoscleromatis Klebsiella terrigena Kluyvera ascorbata Kluyvera cryocrescens Kluyvera georgiana Kocuria kristinae Lactobacillus acidophilus Lactobacillus garvieae Lactobacillus paracasei Lactobacillus casei subsp. casei Lactococcus garvieae Lactococcus lactis Lactococcus lactis subsp. lactis Legionella micdadei Legionella pneumophila subsp. pneumophila Leminorella grimontii Leminorella richardii Leptospira biflexa Leptospira interrogans Leuconostoc mesenteroides subsp. dextranicum Listeria innocua Listeria ivanovii Listeria monocytogenes Listeria seeligeri Macrococcus caseolyticus Magnetospirillum magnetotacticum Megamonas hypermegale Methanobacterium thermoautotrophicum Methanococcus jannaschii Methanococcus vannielii Methanosarcina barkeri Methanosarcina jannaschii Methylobacillus flagellatum Methylomonas clara Micrococcus luteus Micrococcus lylae Mitsuokella multacidus Mobiluncus curtisii subsp. holmesii Moellerella thermoacetica Moellerella wisconsensis Moorella thermoacetica Moraxella catarrhalis Moraxella osloensis Morganella morganii subsp. morganii Mycobacterium avium Mycobacterium bovis Mycobacterium gordonae Mycobacterium kansasii Mycobacterium leprae Mycobacterium terrae Mycobacterium tuberculosis Mycoplasma capricolum Mycoplasma gallisepticum Mycoplasma genitalium Mycoplasma hominis Mycoplasma pirum Mycoplasma mycoides Mycoplasma pneumoniae Mycoplasma pulmonis Mycoplasma salivarium Myxococcus xanthus Neisseria animalis Neisseria canis Neisseria cinerea Neisseria cuniculi Neisseria elongata subsp. elongata Neisseria elongata subsp. intermedia Neisseria flava Neisseria flavescens Neisseria gonorrhoeae Neisseria lactamica Leclercia adecarboxylata Neisseria meningitidis Neisseria mucosa Neisseria perflava Neisseria pharyngis var. flava Neisseria polysaccharea Neisseria sicca Neisseria subflava Neisseria weaveri Obesumbacterium proteus Ochrobactrum anthropi Pantoea agglomerans Pantoea dispersa Paracoccus denitrificans Pasteurella multocida Pectinatus frisingensis Peptococcus niger Peptostreptococcus anaerobius Peptostreptococcus asaccharolyticus Peptostreptococcus prevotii Phormidium ectocarpi Pirellula marina Planobispora rosea Plesiomonas shigelloides Plectonema boryanum Porphyromonas asaccharolytica Porphyromonas gingivalis Pragia fontium Prevotella buccalis Prevotella melaninogenica Prevotella oralis Prevotella ruminocola Prochlorothrix hollandica Propionibacterium acnes Propionigenium modestum Proteus mirabilis Proteus penneri Proteus vulgaris Providencia alcalifaciens Providencia rettgeri Providencia rustigianii Providencia stuartii Pseudomonas aeruginosa Pseudomonas fluorescens Pseudomonas putida Pseudomonas stutzeri Psychrobacter phenylpyruvicum Pyrococcus abyssi Rahnella aquatilis Rickettsia prowazekii Rhizobium leguminosarum Rhizobium phaseoli Rhodobacter capsulatus Rhodobacter sphaeroides Rhodopseudomonas palustris Rhodospirillum rubrum Ruminococcus albus Ruminococcus bromii Salmonella bongori Salmonella choleraesuis subsp. arizonae Salmonella choleraesuis subsp choleraesuis Salmonella choleraesuis subsp. diarizonae Salmonella choleraesuis subsp. houtenae Salmonella choleraesuis subsp. indica Salmonella choleraesuis subsp. salamae Serpulina hyodysenteriae Serratia ficaria Serratia fonticola Serratia grimesii Serratia liquefaciens Serratia marcescens Serratia odorifera Serratia plymuthica Serratia rubidaea Shewanella putrefaciens Shigella boydii Shigella dysenteriae Shigella flexneri Shigella sonnei Sinorhizobium meliloti Spirochaeta aurantia Staphylococcus aureus Staphylococcus aureus subsp. aureus Staphylococcus auricularis Staphylococcus capitis subsp. capitis Staphylococcus cohnii subsp. cohnii Staphylococcus epidermidis Staphylococcus haemolyticus Staphylococcus hominis Staphylococcus hominis subsp. hominis Staphylococcus lugdunensis Staphylococcus saprophyticus Staphylococcus sciuri subsp. sciuri Staphylococcus simulans Staphylococcus warneri Stigmatella aurantiaca Stenotrophomonas maltophilia Streptococcus acidominimus Streptococcus agalactiae Streptococcus anginosus Streptococcus bovis Streptococcus cricetus Streptococcus cristatus Streptococcus downei Streptococcus dysgalactiae Streptococcus equi subsp. equi Streptococcus ferus Streptococcus gordonii Streptococcus macacae Streptococcus mitis Streptococcus mutans Streptococcus oralis Streptococcus parasanguinis Streptococcus pneumoniae Streptococcus pyogenes Streptococcus ratti Streptococcus salivarius Streptococcus salivarius subsp. thermophilus Streptococcus sanguinis Streptococcus sobrinus Streptococcus suis Streptococcus uberis Streptococcus vestibularis Streptomyces anbofaciens Streptomyces aureofaciens Streptomyces cinnamoneus Streptomyces coelicolor Streptomyces collinus Streptomyces lividans Streptomyces netropsis Streptomyces ramocissimus Streptomyces rimosus Streptomyces venezuelae Succinivibrio dextrinosolvens Synechococcus sp. Synechocystis sp. Tatumella ptyseos Taxeobacter occealus Tetragenococcus halophilus Thermoplasma acidophilum Thermotoga maritima Thermus aquaticus Thermus thermophilus Thiobacillus ferrooxidans Thiomonas cuprina Trabulsiella guamensis Treponema pallidum Ureaplasma urealyticum Veillonella parvula Vibrio alginolyticus Vibrio anguillarum Vibrio cholerae Vibrio mimicus Wolinella succinogenes Xanthomonas citri Xanthomonas oryzae Xenorhabdus bovieni Xenorhabdus nematophilus Yersinia bercovieri Yersinia enterocolitica Yersinia frederiksensii Yersinia intermedia Yersinia pestis Yersinia pseudotuberculosis Yersinia rohdei Yokenella regensburgei Zoogloea ramigera

TABLE 4 Example of microbial species for which tuf and/or atpD and/or recA nucleic acids and/or sequences are used in the present invention (continued) Fungal species Absidia corymbifera Absidia glauca Alternaria alternate Arxula adeninivorans Aspergillus flavus Aspergillus fumigatus Aspergillus nidulans Aspergillus niger Aspergillus oryzae Aspergillus terreus Aspergillus versicolor Aureobasidium pullulans Basidiobolus ranarum Bipolaris hawaiiensis Bilophila wadsworthia Blastoschizomyces capitatus Blastomyces dermatitidis Candida albicans Candida catenulata Candida dubliniensis Candida famata Candida glabrata Candida guilliermondii Candida haemulonii Candida inconspicua Candida kefyr Candida krusei Candida lambica Candida lusitaniae Candida norvegica Candida norvegensis Candida parapsilosis Candida rugosa Candida sphaerica Candida tropicalis Candida utilis Candida viswanathii Candida zeylanoides Cladophialophora carrionii Coccidioides immitis Coprinus cinereus Cryptococcus albidus Cryptococcus humicolus Cryptococcus laurentii Cryptococcus neoformans Cunninghamella bertholletiae Curvularia lunata Emericella nidulans Emmonsia parva Eremothecium gossypii Exophiala dermatitidis Exophiala jeanselmei Exophiala moniliae Exserohilum rostratum Eremothecium gossypii Fonsecaea pedrosoi Fusarium moniliforme Fusarium oxysporum Fusarium solani Geotrichum sp. Histoplasma capsulatum Hortaea werneckii Issatchenkia orientalis Kudrjanzev Kluyveromyces lactis Malassezia furfur Malassezia pachydermatis Malbranchea filamentosa Metschnikowia pulcherrima Microsporum audouinii Microsporum canis Mucor circinelloides Neurospora crassa Paecilomyces lilacinus Paracoccidioides brasiliensis Penicillium marneffei Phialaphora verrucosa Pichia anomala Piedraia hortai Podospora anserina Podospora curvicolla Puccinia graminis Pseudallescheria boydii Reclinomonas americana Rhizomucor racemosus Rhizopus oryzae Rhodotorula minuta Rhodotorula mucilaginosa Saccharomyces cerevisiae Saksenaea vasiformis Schizosaccharomyces pombe Scopulariopsis koningii Sordaria macrospora Sporobolomyces salmonicolor Sporothrix schenckii Stephanoascus ciferrii Syncephalastrum racemosum Trichoderma reesei Trichophyton mentagrophytes Trichophyton rubrum Trichophyton tonsurans Trichosporon cutaneum Ustilago maydis Wangiella dermatitidis Yarrowia lipolytica Parasitical species Babesia bigemina Babesia bovis Babesia microti Blastocystis hominis Crithidia fasciculata Cryptosporidium parvum Entamoeba histolytica Giardia lamblia Kentrophoros sp. Leishmania aethiopica Leishmania amazonensis Leishmania braziliensis Leishmania donovani Leishmania infantum Leishmania enriettii Leishmania gerbilli Leishmania guyanensis Leishmania hertigi Leishmania major Leishmania mexicana Leishmania panamensis Leishmania tarentolae Leishmania tropica Neospora caninum Onchocerca volvulus Plasmodium berghei Plasmodium falciparum Plasmodium knowlesi Porphyra purpurea Toxoplasma gondii Treponema pallidum Trichomonas tenax Trichomonas vaginalis Trypanosoma brucei Trypanosoma brucei subsp. brucei Trypanosoma congolense Trypanosoma cruzi

TABLE 5 Antimicrobial agents resistance genes selected for diagnostic purposes SEQ Gene Antimicrobial agent Bacteria¹ ACCESSION NO. ID NO. aac(3)-Ib² Aminoglycosides Enterobacteriaceae L06157 Pseudomonads aac(3)-IIb² Aminoglycosides Enterobacteriaceae, M97172 Pseudomonads aac(3)-IVa² Aminoglycosides Enterobacteriaceae X01385 aac(3)-VIa² Aminoglycosides Enterobacteriaceae, M88012 Pseudomonads aac(2′)-1a² Aminoglycosides Enterobacteriaceae, X04555 Pseudomonads aac(6′)-aph(2″)² Aminoglycosides Enterococcus sp., 83-86³ Staphylococcus sp. aac(6′)-Ia,² Aminoglycosides Enterobacteriaceae, M18967 Pseudomonads aac(6′)-Ic² Aminoglycosides Enterobacteriaceae, M94066 Pseudomonads aac(6′)-IIa² Aminoglycosides Pseudomonads 112⁴ aadB [ant(2″)-Ia²] Aminoglycosides Enterobacteriaceae 53-54³ aacC1 [aac(3)-Ia²] Aminoglycosides Pseudomonads 55-56³ aacC2 [aac(3)-IIa²] Aminoglycosides Pseudomonads 57-58³ aacC3 [aac(3)-III²] Aminoglycosides Pseudomonads 59-60³ aacA4 [aac(6′)-Ib²] Aminoglycosides Pseudomonads 65-66³ ant(3″)-Ia² Aminoglycosides Enterobacteriaceae, X02340 Enterococcus sp., M10241 Staphylococcus sp. ant(4′)-Ia² Aminoglycosides Staphylococcus sp. V01282 aph(3′)-Ia² Aminoglycosides Enterobacteriaceae, J01839 Pseudomonads aph(3′)-IIa² Aminoglycosides Enterobacteriaceae, V00618 Pseudomonads aph(3′)-IIIa² Aminoglycosides Enterococcus sp., V01547 Staphylococcus sp. aph(3′)-VIa² Aminoglycosides Enterobacteriaceae, X07753 Pseudomonads rpsL² Streptomycin M. tuberculosis, X80120 M. avium complex U14749 X70995 L08011 bla_(OXA) ^(5,6) β-lactams Enterobacteriaceae, Y10693 110⁴ Pseudomonads AJ238349 AJ009819 X06046 X03037 X07260 U13880 X75562 AF034958 J03427 Z22590 U59183 L38523 U63835 AF043100 AF060206 U85514 AF043381 AF024602 AF064820 bla_(ROB) ⁵ β-lactams Haemophilus sp. 45-48³ bla_(SHV) ^(5,6) β-lactams Enterobacteriacea, AF124984 41-44³ Pseudomonas aeruginosa AF148850 M59181 X98099 M33655 AF148851 X53433 L47119 AF074954 X53817 AF096930 X55640 Y11069 U20270 U92041 S82452 X98101 X98105 AF164577 AJ011428 AF116855 AB023477 AF293345 AF227204 AF208796 AF132290 bla_(TEM) ^(5,6) β-lactams Enterobacteriaceae, AF012911 37-40³ Neisseria sp., U48775 Haemophilus sp. AF093512 AF052748 X64523 Y13612 X57972 AF157413 U31280 U36911 U48775 V00613 X97254 AJ012256 X04515 AF126482 U09188 M88143 Y14574 AF188200 AJ251946 Y17581 Y17582 Y17583 M88143 U37195 Y17584 X64523 U95363 Y10279 Y10280 Y10281 AF027199 AF104441 AF104442 AF062386 X57972 AF047171 AF188199 AF157553 AF190694 AF190695 AF190693 AF190692 bla_(SHV) ^(5,6) β-lactams Enterobacteriacea, AF124984 41-44³ Pseudomonas aeruginosa AF148850 M59181 X98099 M33655 AF148851 X53433 L47119 AF074954 X53817 AF096930 X55640 Y11069 U20270 U92041 S82452 X98101 X98105 AF164577 AJ011428 AF116855 AB023477 AF293345 AF227204 AF208796 AF132290 bla_(TEM) ^(5,6) β-lactams Enterobacteriaceae, AF012911 37-40³ Neisseria sp., U48775 Haemophilus sp. AF093512 AF052748 X64523 Y13612 X57972 AF157413 U31280 U36911 U48775 V00613 X97254 AJ012256 X04515 AF126482 U09188 M88143 Y14574 AF188200 AJ251946 Y17581 Y17582 Y17583 M88143 U37195 Y17584 X64523 U95363 Y10279 Y10280 Y10281 AF027199 AF104441 AF104442 AF062386 X57972 AF047171 AF188199 AF157553 AF190694 AF190695 AF190693 AF190692 bla_(CARB) ⁵ β-lactams Pseudomonas sp., J05162 Enterobacteriaceae S46063 M69058 U14749 D86225 D13210 Z18955 AF071555 AF153200 AF030945 bla_(CTX-M-1) ⁵ β-lactams Enterobacteriaceae X92506 bla_(CTX-M-2) ⁵ β-lactams Enterobacteriaceae X92507 bla_(CMY-2) ⁷ β-lactams Enterobacteriaceae X91840 AJ007826 AJ011293 AJ011291 Y17716 Y16783 Y16781 Y15130 U77414 S83226 Y15412 X78117 bla_(IMP) ⁵ β-lactams Enterobacteriaceae, AJ223604 Pseudomonas aeruginosa S71932 D50438 D29636 X98393 AB010417 D78375 bla_(PER-1) ⁵ β-lactams Enterobacteriaceae, Z21957 Pseudomodanaceae bla_(PER-2) ⁷ β-lactams Enterobacteriaceae X93314 blaZ¹² β-lactams Enterococcus sp., 111⁴ Staphylococcus sp. mecA¹² β-lactams Staphylococcus sp. 97-98³ pbp1a¹³ β-lactams Streptococcus pneumoniae M90527 1004-1018, X67872 1648, 2056-2064, AB006868 2273-2276 AB006874 X67873 AB006878 AB006875 AB006877 AB006879 AF046237 AF046235 AF026431 AF046232 AF046233 AF046236 X67871 Z49095 AF046234 AB006873 X67866 X67868 AB006870 AB006869 AB006872 X67870 AB006871 X67867 X67869 AB006876 AF046230 AF046238 Z49094 pbp2b¹³ β-lactams Streptococcus pneumoniae X16022 1019-1033 M25516 M25518 M25515 U20071 U20084 U20082 U20067 U20079 Z22185 U20072 pbp2b¹³ β-lactams Streptococcus pneumoniae U20083 U20081 M25522 U20075 U20070 U20077 U20068 Z22184 U20069 U20078 M25521 M25525 M25519 Z21981 M25523 M25526 U20076 U20074 M25520 M25517 M25524 Z22230 U20073 U20080 pbp2x¹³ β-lactams Streptococcus pneumoniae X16367 1034-1048 X65135 AB011204 AB011209 AB011199 AB011200 AB011201 AB011202 AB011198 AB011208 AB011205 AB015852 AB011210 AB015849 AB015850 AB015851 AB015847 AB015846 AB011207 AB015848 Z49096 int β-lactams, Enterobacteriaceae, 99-102³ trimethoprim sul aminoglycosides, Pseudomonads 103-106³ antiseptic, chloramphenicol ermA¹⁴ Macrolides, Staphylococcus sp. 113⁴ lincosamides, streptogramin B ermB¹⁴ Macrolides, Enterobacteriaceae, 114⁴ lincosamides, Staphylococcus sp. streptogramin B Enterococcus sp. Streptococcus sp. ermC¹⁴ Macrolides, Enterobacteriaceae, 115⁴ lincosamides, Staphylococcus sp. streptogramin B ereA¹² Macrolides Enterobacteriaceae, M11277 Staphylococcus sp. E01199 AF099140 ereB¹² Macrolides Enterobacteriaceae A15097 Staphylococcus sp. X03988 msrA¹² Macrolides Staphylococcus sp. 77-80³ mefA, mefE⁸ Macrolides Streptococcus sp. U70055 U83667 mphA⁸ Macrolides Enterobacteriaceae, D16251 Staphylococcus sp. U34344 U36578 linA/linA′⁹ Lincosamides Staphylococcus sp. J03947 M14039 A15070 E01245 linB¹⁰ Lincosamides Enterococcus faecium AF110130 AJ238249 vga¹⁵ Streptrogramin Staphylococcus sp. M90056 89-90³ U82085 vgb¹⁵ Streptrogramin Staphylococcus sp. M36022 M20219 AF015628 vat¹⁵ Streptrogramin Staphylococcus sp. L07778 87-88³ vatB¹⁵ Streptrogramin Staphylococcus sp. U19459 L38809 satA¹⁵ Streptrogramin Enterococcus faecium L12033 81-82³ mupA¹² Mupirocin Staphylococcus aureus X75439 X59478 X59477 gyrA¹⁶ Quinolones Gram-positive and X95718 1255, 1607-1608, gram-negative bacteria X06744 1764-1776, X57174 2013-2014, X16817 2277-2280 X71437 AF065152 AF060881 D32252 parC/grlA¹⁶ Quinolones Gram-positive and AB005036 1777-1785 gram-negative bacteria AF056287 X95717 AF129764 AB017811 AF065152 parE/grlB¹⁶ Quinolones Gram-positive bacteria X95717 AF065153 AF058920 norA¹⁶ Quinolones Staphylococcus sp. D90119 M80252 M97169 mexR (nalB)¹⁶ Quinolones Pseudomonas aeruginosa U23763 nfxB¹⁶ Quinolones Pseudomonas aeruginosa X65646 cat¹² Chloramphenicol Gram-positive and M55620 gram-negative bacteria X15100 A24651 M28717 A00568 A00569 X74948 Y00723 A24362 A00569 M93113 M62822 M58516 V01277 X02166 M77169 X53796 J01841 X07848 ppflo-like Chloramphenicol AF071555 embB¹⁷ Ethambutol Mycobacterium tuberculosis U68480 pncA¹⁷ Pyrazinamide Mycobacterium tuberculosis U59967 rpoB¹⁷ Rifampin Mycobacterium tuberculosis AF055891 AF055892 S71246 L27989 AF055893 inhA¹⁷ Isoniazid Mycobacterium tuberculosis AF106077 U02492 vanA¹² Vancomycin Enterococcus sp. 67-70³ 1049-1057 vanB¹² Vancomycin Enterococcus sp. 116⁴ vanC1¹² Vancomycin Enterococcus gallinarum 117⁴ 1058-1059 vanC2¹² Vancomycin Enterococcus casseliflavus U94521 1060-1063 U94522 U94523 U94524 U94525 L29638 vanC3¹² Vancomycin Enterococcus flavescens L29639 1064-1066 U72706 vanD¹⁸ Vancomycin Enterococcus faecium AF130997 vanE¹² Vancomycin Enterococcus faecium AF136925 tetB¹⁹ Tetracycline Gram-negative bacteria J01830 AF162223 AP000342 S83213 U81141 V00611 tetM¹⁹ Tetracycline Gram-negative and X52632 Gram-positive bacteria AF116348 U50983 X92947 M211136 U08812 X04388 sul II²⁰ Sulfonamides Gram-negative bacteria M36657 AF017389 AF017391 dhfrIa²⁰ Trimethoprim Gram-negative bacteria AJ238350 X17477 K00052 U09476 X00926 dhfrIb²⁰ Trimethoprim Gram-negative bacteria Z50805 Z50804 dhfrV²⁰ Trimethoprim Gram-negative bacteria X12868 dhfrVI²⁰ Trimethoprim Gram-negative bacteria Z86002 dhfrVII²⁰ Trimethoprim Gram-negative bacteria U31119 AF139109 X58425 dhfrVIII²⁰ Trimethoprim Gram-negative bacteria U10186 U09273 dhfrIX²⁰ Trimethoprim Gram-negative bacteria X57730 dhfrXII²⁰ Trimethoprim Gram-negative bacteria Z21672 AF175203 AF180731 M84522 dhfrXIII²⁰ Trimethoprim Gram-negative bacteria Z50802 dhfrXV²⁰ Trimethoprim Gram-negative bacteria Z83331 dhfrXVII²⁰ Trimethoprim Gram-negative bacteria AF170088 AF180469 AF169041 dfrA²⁰ Trimethoprim Staphylococcus sp. AF045472 U40259 AF051916 X13290 Y07536 Z16422 Z48233 ¹Bacteria having high incidence for the specified antibiotic resistance gene. The presence of the antibiotic resistance genes in other bacteria is not excluded. ²Shaw, K. J., P. N. Rather, R. S. Hare, and G. H. Miller. 1993. Molecular genetics of aminoglycoside resistance genes and familial relationships of the aminoglycoside-modifying enzymes. Microbial. Rev. 57: 138-163. ³Antibiotic resistance genes from our assigned U.S. Pat. No. 6,001,564 for which we have selected PCR primer pairs. ⁴These SEQ ID NOs. refer to a previous patent (publication WO98/20157). ⁵Bush, K., G. A. Jacoby and A. Medeiros. 1995. A functional classification scheme for β-lactamase and its correlation with molecular structure. Antimicrob. Agents. Chemother. 39: 1211-1233. ⁶Nucleotide mutations in bla_(SHV), bla_(TEM), and bla_(OXA), are associated with extended-spectrum β-lactamase or inhibitor-resistant β-lactamase. ⁷Bauerfeind, A., Y. Chong, and K. Lee. 1998. Plasmid-encoded AmpC beta-lactamases: how far have we gone 10 ears after discovery? Yonsei Med. J. 39: 520-525. ⁸Sutcliffe. J., T. Grebe, A. Tait-Kamradt, and L. Wondrack. 1996. Detection of erythromycin-resistant determinants by PCR. Antimicrob. Agent Chemother. 40: 2562-2566. ⁹Leclerc, R., A., Brisson-Noël, J. Duval, and P. Courvalin. 1991. Phenotypic expression and genetic heterogeneity of lincosamide inactivation in Staphylococcus sp. Antimicrob. Agents. Chemother. 31: 1887-1891. ¹⁰Bozdogan, B., L. Berrezouga, M.-S. Kuo, D. A. Yurek, K. A. Farley, B. J. Stockman, and R. Leclercq. 1999. A new gene, linB, conferring resistance to lincosamides by nucleotidylation in Enterococcus faecium HM1025. Antimicrob. Agents. Chemother. 43: 925-929. ¹¹Cockerill III, F. R. 1999. Genetic methods for assessing antimicrobial resistance. Antimicrob. Agents. Chemother. 43: 199-212. ¹²Tenover, F. C., T. Popovic, and O Olsvik. 1996. Genetic methods for detecting antibacterial resistance genes. pp. 1368-1378. In Murray, P. R., E. J. Baron, M. A. Pfaller, F. C. Tenover, R. H. Yolken (eds). Manual of clinical microbiology. 6th ed., ASM Press, Washington, D. C. USA ¹³Dowson, C. G., T. J. Tracey, and B. G. Spratt. 1994. Origin and molecular epidemiology of penicillin-binding-protein-mediated resistance to β-lactam antibiotics. Trends Molec. Microbiol. 2: 361-366. ¹⁴Jensen, L. B., N. Frimodt-Moller, F. M. Aarestrup. 1999. Presence of erm gene classes in Gram-positive bacteria of animal and human origin in Denmark. FEMS Microbiol. 170: 151-158: ¹⁵Thal, L. A., and M. J. Zervos. 1999. Occurrence and epidemiology of resistance to virginimycin and streptrogramins. J. Antimicrob. Chemother. 43: 171-176. ¹⁶Martinez J. L., A. Alonso, J. M. Gomez-Gomez, and F. Baquero. 1998. Quinolone resistance by mutations in chromosomal gyrase genes. Just the tip of the iceberg? J. Antimicrob. Chemother. 42: 683-688 ¹⁷Cockerill III, F. R. 1999. Genetic methods for assessing antimicrobial resistance. Antimicrob. Agents. Chemother. 43: 199-212. ¹⁸Casadewall, B. and P. Courvalin. 1999 Characterization of the vanD glycopeptide resistance gene cluster from Enterococcus faecium BM 4339. J. Bacteriol. 181: 3644-3648. ¹⁹Roberts, M. C. 1999. Genetic mobility and distribution of tetracycline resistance determinants. Ciba Found. Symp. 207: 206-222. ²⁰Huovinen, P., L. Sundström, G. Swedberg, and O. Sköld. 1995. Trimethoprim and sulfonamide resistance.Antimicrob. Agent Chemother. 39: 279-289.

TABLE 6 List of bacterial toxins selected for diagnostic purposes. Organism Toxin Accession number Actinobacillus actinomycetemcomitans Cytolethal distending toxin (cdtA, cdtB, cdtC) AF006830 Leukotoxin (ltxA) M27399 Actinomyces pyogenes Hemolysin (pyolysin) U84782 Aeromonas hydrophila Aerolysin (aerA) M16495 Haemolysin (hlyA) U81555 Cytotonic enterotoxin (alt) L77573 Bacillus anthracis Anthrax toxin (cya) M23179 Bacillus cereus Enterotoxin (bceT) D17312 AF192766, AF192767 Enterotoxic hemolysin BL AJ237785 Non-haemolytic enterotoxins A, B and C (nhe) Y19005 Bacillus mycoides Hemolytic enterotoxin HBL AJ243150 to AJ243153 Bacillus pseudomycoides Hemolytic enterotoxin HBL AJ243154 to AJ243156 Bacteroides fragilis Enterotoxin (bftP) U67735 Matrix metalloprotease/enterotoxin (fragilysin) S75941, AF038459 Metalloprotease toxin-2 U90931 AF081785 Metalloprotease toxin-3 AF056297 Bordetella bronchiseptica Adenylate cyclase hemolysin (cyaA) Z37112, U22953 Dermonecrotic toxin (dnt) U59687 AB020025 Bordetella pertussis Pertussis toxin (S1 subunit, tox) AJ006151 AJ006153 AJ006155 AJ006157 AJ006159 AJ007363 M14378, M16494 AJ007364 M13223 X16347 Adenyl cyclase (cya) 18323 Dermonecrotic toxin (dnt) U10527 Campylobacter jejuni Cytolethal distending toxin (cdtA, cdtB, cdtC) U51121 Citrobacter freundii Shiga-like toxin (slt-llcA) X67514, S53206 Clostridium botulinum Botulism toxin (BoNT) (A, B, E and F serotypes X52066, X52088 are neurotoxic for humans; the other serotypes X73423 have not been considered) M30196 X70814 X70819 X71343 Z11934 X70817 M81186 X70818 X70815 X62089 X62683 S76749 X81714 X70816 X70820 X70281 L35496 M92906 Clostridium difficile A toxin (enterotoxin) (tcdA) (cdtA) AB012304 AF053400 Y12616 X51797 X17194 M30307 B toxin (cytotoxin) (toxB) (cdtB) Z23277 X53138 Clostridium perfringens Alpha (phospholipase C) (cpa) L43545 L43546 L43547 L43548 X13608 X17300 D10248 Beta (dermonecrotic protein) (cpb) L13198 X83275 L77965 Enterotoxin (cpe) AJ000766 M98037 X81849 X71844 Y16009 Enterotoxin pseudogene (not expressed) AF037328 AF037329 AF037330 Epsilon toxin (etxD) M80837 M95206 X60694 Iota (Ia and Ib) X73562 Lambda (metalloprotease) D45904 Theta (perfringolysin O) M36704 Clostridium sordellii Cytotoxin L X82638 Clostridium tetani Tetanos toxin X06214 X04436 Corynebacterium diphtheriae Diphtheriae toxin X00703 Corynebacterium pseudotuberculosis Phospholipase C A21336 Eikenella corrodens lysine decarboxylase (cadA) U89166 Enterobacter cloacae Shiga-like toxin II Z50754, U33502 Enterococcus faecalis Cytolysin B (cylB) M38052 Escherichia coli (EHEC) Hemolysin toxin (hlyA and ehxA) AF043471 X94129 X79839 X86087 AB011549 AF074613

TABLE 7 Origin of the nucleic acids and/or sequences in the sequence listing. SEQ ID NO. Archaeal, bacterial, fungal or parasitical species Source Gene* 1 Acinetobacter baumannii This patent tuf 2 Actinomyces meyeri This patent tuf 3 Aerococcus viridans This patent tuf 4 Achromobacter xylosoxidans subsp. denitrificans This patent tuf 5 Anaerorhabdus furcosus This patent tuf 6 Bacillus anthracis This patent tuf 7 Bacillus cereus This patent tuf 8 Bacteroides distasonis This patent tuf 9 Enterococcus casseliflavus This patent tuf 10 Staphylococcus saprophyticus This patent tuf 11 Bacteroides ovatus This patent tuf 12 Bartonella henselae This patent tuf 13 Bifidobacterium adolescentis This patent tuf 14 Bifidobacterium dentium This patent tuf 15 Brucella abortus This patent tuf 16 Burkholderia cepacia This patent tuf 17 Cedecea davisae This patent tuf 18 Cedecea neteri This patent tuf 19 Cedecea lapagei This patent tuf 20 Chlamydia pneumoniae This patent tuf 21 Chlamydia psittaci This patent tuf 22 Chlamydia trachomatis This patent tuf 23 Chryseobacterium meningosepticum This patent tuf 24 Citrobacter amalonaticus This patent tuf 25 Citrobacter braakii This patent tuf 26 Citrobacter koseri This patent tuf 27 Citrobacter farmeri This patent tuf 28 Citrobacter freundii This patent tuf 29 Citrobacter sedlakii This patent tuf 30 Citrobacter werkmanii This patent tuf 31 Citrobacter youngae This patent tuf 32 Clostridium perfringens This patent tuf 33 Comamonas acidovorans This patent tuf 34 Corynebacterium bovis This patent tuf 35 Corynebacterium cervicis This patent tuf 36 Corynebacterium flavescens This patent tuf 37 Corynebacterium kutscheri This patent tuf 38 Corynebacterium minutissimum This patent tuf 39 Corynebacterium mycetoides This patent tuf 40 Corynebacterium pseudogenitalium This patent tuf 41 Corynebacterium renale This patent tuf 42 Corynebacterium ulcerans This patent tuf 43 Corynebacterium urealyticum This patent tuf 44 Corynebacterium xerosis This patent tuf 45 Coxiella burnetii This patent tuf 46 Edwardsiella hoshinae This patent tuf 47 Edwardsiella tarda This patent tuf 48 Eikenella corrodens This patent tuf 49 Enterobacter aerogenes This patent tuf 50 Enterobacter agglomerans This patent tuf 51 Enterobacter amnigenus This patent tuf 52 Enterobacter asburiae This patent tuf 53 Enterobacter cancerogenus This patent tuf 54 Enterobacter cloacae This patent tuf 55 Enterobacter gergoviae This patent tuf 56 Enterobacter hormaechei This patent tuf 57 Enterobacter sakazakii This patent tuf 58 Enterococcus casseliflavus This patent tuf 59 Enterococcus cecorum This patent tuf 60 Enterococcus dispar This patent tuf 61 Enterococcus durans This patent tuf 62 Enterococcus faecalis This patent tuf 63 Enterococcus faecalis This patent tuf 64 Enterococcus faecium This patent tuf 65 Enterococcus flavescens This patent tuf 66 Enterococcus gallinarum This patent tuf 67 Enterococcus hirae This patent tuf 68 Enterococcus mundtii This patent tuf 69 Enterococcus pseudoavium This patent tuf 70 Enterococcus raffinosus This patent tuf 71 Enterococcus saccharolyticus This patent tuf 72 Enterococcus solitarius This patent tuf 73 Enterococcus casseliflavus This patent tuf (C) 74 Staphylococcus saprophyticus This patent unknown 75 Enterococcus flavescens This patent tuf (C) 76 Enterococcus gallinarum This patent tuf (C) 77 Ehrlichia canis This patent tuf 78 Escherichia coli This patent tuf 79 Escherichia fergusonii This patent tuf 80 Escherichia hermannii This patent tuf 81 Escherichia vulneris This patent tuf 82 Eubacterium lentum This patent tuf 83 Eubacterium nodatum This patent tuf 84 Ewingella americana This patent tuf 85 Francisella tularensis This patent tuf 86 Fusobacterium nucleatum subsp. polymorphum This patent tuf 87 Gemella haemolysans This patent tuf 88 Gemella morbillorum This patent tuf 89 Haemophilus actinomycetemcomitans This patent tuf 90 Haemophilus aphrophilus This patent tuf 91 Haemophilus ducreyi This patent tuf 92 Haemophilus haemolyticus This patent tuf 93 Haemophilus parahaemolyticus This patent tuf 94 Haemophilus parainfluenzae This patent tuf 95 Haemophilus paraphrophilus This patent tuf 96 Haemophilus segnis This patent tuf 97 Hafnia alvei This patent tuf 98 Kingella kingae This patent tuf 99 Klebsiella omithinolytica This patent tuf 100 Klebsiella oxytoca This patent tuf 101 Klebsiella planticola This patent tuf 102 Klebsiella pneumoniae subsp. ozaenae This patent tuf 103 Klebsiella pneumoniae pneumoniae This patent tuf 104 Klebsiella pneumoniae subsp. rhinoscleromatis This patent tuf 105 Kluyvera ascorbata This patent tuf 106 Kluyvera cryocrescens This patent tuf 107 Kluyvera georgiana This patent tuf 108 Lactobacillus casei subsp. casei This patent tuf 109 Lactococcus lactis subsp. lactis This patent tuf 110 Leclercia adecarboxylata This patent tuf 111 Legionella micdadei This patent tuf 112 Legionella pneumophila subsp. pneumophila This patent tuf 113 Leminorella grimontii This patent tuf 114 Leminorella richardii This patent tuf 115 Leptospira interrogans This patent tuf 116 Megamonas hypermegale This patent tuf 117 Mitsuokella multacidus This patent tuf 118 Mobiluncus curtisii subsp. holmesii This patent tuf 119 Moellerella wisconsensis This patent tuf 120 Moraxella catarrhalis This patent tuf 121 Morganella morganii subsp. morganii This patent tuf 122 Mycobacterium tuberculosis This patent tuf 123 Neisseria cinerea This patent tuf 124 Neisseria elongata subsp. elongata This patent tuf 125 Neisseria flavescens This patent tuf 126 Neisseria gonorrhoeae This patent tuf 127 Neisseria lactamica This patent tuf 128 Neisseria meningitidis This patent tuf 129 Neisseria mucosa This patent tuf 130 Neisseria sicca This patent tuf 131 Neisseria subflava This patent tuf 132 Neisseria weaveri This patent tuf 133 Ochrobactrum anthropi This patent tuf 134 Pantoea agglomerans This patent tuf 135 Pantoea dispersa This patent tuf 136 Pasteurella multocida This patent tuf 137 Peptostreptococcus anaerobius This patent tuf 138 Peptostreptococcus asaccharolyticus This patent tuf 139 Peptostreptococcus prevotii This patent tuf 140 Porphyromonas asaccharolytica This patent tuf 141 Porphyromonas gingivalis This patent tuf 142 Pragia fontium This patent tuf 143 Prevotella melaninogenica This patent tuf 144 Prevotella oralis This patent tuf 145 Propionibacterium acnes This patent tuf 146 Proteus mirabilis This patent tuf 147 Proteus penneri This patent tuf 148 Proteus vulgaris This patent tuf 149 Providencia alcalifaciens This patent tuf 150 Providencia rettgeri This patent tuf 151 Providencia rustigianii This patent tuf 152 Providencia stuartii This patent tuf 153 Pseudomonas aeruginosa This patent tuf 154 Pseudomonas fluorescens This patent tuf 155 Pseudomonas stutzeri This patent tuf 156 Psychrobacter phenylpyruvicum This patent tuf 157 Rahnella aquatilis This patent tuf 158 Salmonella choleraesuis subsp. arizonae This patent tuf 159 Salmonella choleraesuis subsp. choleraesuis This patent tuf serotype Choleraesuis 160 Salmonella choleraesuis subsp. diarizonae This patent tuf 161 Salmonella choleraesuis subsp. choleraesuis This patent tuf serotype Heidelberg 162 Salmonella choleraesuis subsp. houtenae This patent tuf 163 Salmonella choleraesuis subsp. indica This patent tuf 164 Salmonella choleraesuis subsp. salamae This patent tuf 165 Salmonella choleraesuis subsp. choleraesuis serotype Typhi This patent tuf 166 Serratia fonticola This patent tuf 167 Serratia liquefaciens This patent tuf 168 Serratia marcescens This patent tuf 169 Serratia odorifera This patent tuf 170 Serratia plymuthica This patent tuf 171 Serratia rubidaea This patent tuf 172 Shigella boydii This patent tuf 173 Shigella dysenteriae This patent tuf 174 Shigella flexneri This patent tuf 175 Shigella sonnei This patent tuf 176 Staphylococcus aureus This patent tuf 177 Staphylococcus aureus This patent tuf 178 Staphylococcus aureus This patent tuf 179 Staphylococcus aureus This patent tuf 180 Staphylococcus aureus subsp. aureus This patent tuf 181 Staphylococcus auricularis This patent tuf 182 Staphylococcus capitis subsp. capitis This patent tuf 183 Macrococcus caseolyticus This patent tuf 184 Staphylococcus cohnii subsp. cohnii This patent tuf 185 Staphylococcus epidermidis This patent tuf 186 Staphylococcus haemolyticus This patent tuf 187 Staphylococcus warneri This patent tuf 188 Staphylococcus haemolyticus This patent tuf 189 Staphylococcus haemolyticus This patent tuf 190 Staphylococcus haemolyticus This patent tuf 191 Staphylococcus hominis subsp. hominis This patent tuf 192 Staphylococcus warneri This patent tuf 193 Staphylococcus hominis This patent tuf 194 Staphylococcus hominis This patent tuf 195 Staphylococcus hominis This patent tuf 196 Staphylococcus hominis This patent tuf 197 Staphylococcus lugdunensis This patent tuf 198 Staphylococcus saprophyticus This patent tuf 199 Staphylococcus saprophyticus This patent tuf 200 Staphylococcus saprophyticus This patent tuf 201 Staphylococcus sciuri subsp. sciuri This patent tuf 202 Staphylococcus warneri This patent tuf 203 Staphylococcus warneri This patent tuf 204 Bifidobacterium longum This patent tuf 205 Stenotrophomonas maltophilia This patent tuf 206 Streptococcus acidominimus This patent tuf 207 Streptococcus agalactiae This patent tuf 208 Streptococcus agalactiae This patent tuf 209 Streptococcus agalactiae This patent tuf 210 Streptococcus agalactiae This patent tuf 211 Streptococcus anginosus This patent tuf 212 Streptococcus bovis This patent tuf 213 Streptococcus anginosus This patent tuf 214 Streptococcus cricetus This patent tuf 215 Streptococcus cristatus This patent tuf 216 Streptococcus downei This patent tuf 217 Streptococcus dysgalactiae This patent tuf 218 Streptococcus equi subsp. equi This patent tuf 219 Streptococcus ferus This patent tuf 220 Streptococcus gordonii This patent tuf 221 Streptococcus anginosus This patent tuf 222 Streptococcus macacae This patent tuf 223 Streptococcus gordonii This patent tuf 224 Streptococcus mutans This patent tuf 225 Streptococcus parasanguinis This patent tuf 226 Streptococcus ratti This patent tuf 227 Streptococcus sanguinis This patent tuf 228 Streptococcus sobrinus This patent tuf 229 Streptococcus suis This patent tuf 230 Streptococcus uberis This patent tuf 231 Streptococcus vestibularis This patent tuf 232 Tatumella ptyseos This patent tuf 233 Trabulsiella guamensis This patent tuf 234 Veillonella parvula This patent tuf 235 Yersinia enterocolitica This patent tuf 236 Yersinia frederiksenii This patent tuf 237 Yersinia intermedia This patent tuf 238 Yersinia pestis This patent tuf 239 Yersinia pseudotuberculosis This patent tuf 240 Yersinia rohdei This patent tuf 241 Yokenella regensburgei This patent tuf 242 Achromobacter xylosoxidans subsp. denitrificans This patent atpD 243 Acinetobacter baumannii This patent atpD 244 Acinetobacter lwoffii This patent atpD 245 Staphylococcus saprophyticus This patent atpD 246 Alcaligenes faecalis subsp. faecalis This patent atpD 247 Bacillus anthracis This patent atpD 248 Bacillus cereus This patent atpD 249 Bacteroides distasonis This patent atpD 250 Bacteroides ovatus This patent atpD 251 Leclercia adecarboxylata This patent atpD 252 Stenotrophomonas maltophilia This patent atpD 253 Bartonella henselae This patent atpD 254 Bifidobacterium adolescentis This patent atpD 255 Brucella abortus This patent atpD 256 Cedecea davisae This patent atpD 257 Cedecea lapagei This patent atpD 258 Cedecea neteri This patent atpD 259 Chryseobacterium meningosepticum This patent atpD 260 Citrobacter amalonaticus This patent atpD 261 Citrobacter braakii This patent atpD 262 Citrobacter koseri This patent atpD 263 Citrobacter farmeri This patent atpD 264 Citrobacter freundii This patent atpD 265 Citrobacter koseri This patent atpD 266 Citrobacter sedlakii This patent atpD 267 Citrobacter werkmanii This patent atpD 268 Citrobacter youngae This patent atpD 269 Clostridium innocuum This patent atpD 270 Clostridium perfringens This patent atpD 272 Corynebacterium diphtheriae This patent atpD 273 Corynebacterium pseudodiphtheriticum This patent atpD 274 Corynebacterium ulcerans This patent atpD 275 Corynebacterium urealyticum This patent atpD 276 Coxiella burnetii This patent atpD 277 Edwardsiella hoshinae This patent atpD 278 Edwardsiella tarda This patent atpD 279 Eikenella corrodens This patent atpD 280 Enterobacter agglomerans This patent atpD 281 Enterobacter arnnigenus This patent atpD 282 Enterobacter asburiae This patent atpD 283 Enterobacter cancerogenus This patent atpD 284 Enterobacter cloacae This patent atpD 285 Enterobacter gergoviae This patent atpD 286 Enterobacter hormaechei This patent atpD 287 Enterobacter sakazakii This patent atpD 288 Enterococcus avium This patent atpD 289 Enterococcus casseliflavus This patent atpD 290 Enterococcus durans This patent atpD 291 Enterococcus faecalis This patent atpD 292 Enterococcus faecium This patent atpD 293 Enterococcus gallinarum This patent atpD 294 Enterococcus saccharolyticus This patent atpD 295 Escherichia fergusonii This patent atpD 296 Escherichia hermannii This patent atpD 297 Escherichia vulneris This patent atpD 298 Eubacterium lentum This patent atpD 299 Ewingella americana This patent atpD 300 Francisella tularensis This patent atpD 301 Fusobacterium gonidiaformans This patent atpD 302 Fusobacterium necrophorum subsp. necrophorum This patent atpD 303 Fusobacterium nucleatum subsp. polymorphum This patent atpD 304 Gardnerella vaginalis This patent atpD 305 Gemella haemolysans This patent atpD 306 Gemella morbillorum This patent atpD 307 Haemophilus ducreyi This patent atpD 308 Haemophilus haemolyticus This patent atpD 309 Haemophilus parahaemolyticus This patent atpD 310 Haemophilus parainfluenzae This patent atpD 311 Hafnia alvei This patent atpD 312 Kingella kingae This patent atpD 313 Klebsiella pneumoniae subsp. ozaenae This patent atpD 314 Klebsiella omithinolytica This patent atpD 315 Klebsiella oxytoca This patent atpD 316 Klebsiella planticola This patent atpD 317 Klebsiella pneumoniae subsp. pneumoniae This patent atpD 318 Kluyvera ascorbata This patent atpD 319 Kluyvera cryocrescens This patent atpD 320 Kluyvera georgiana This patent atpD 321 Lactobacillus acidophilus This patent atpD 322 Legionella pneumophila subsp. pneumophila This patent atpD 323 Leminorella grimontii This patent atpD 324 Listeria monocytogenes This patent atpD 325 Micrococcus lylae This patent atpD 326 Moellerella wisconsensis This patent atpD 327 Moraxella catarrhalis This patent atpD 328 Moraxella osloensis This patent atpD 329 Morganella morganii subsp. morganii This patent atpD 330 Pantoea agglomerans This patent atpD 331 Pantoea dispersa This patent atpD 332 Pasteurella multocida This patent atpD 333 Pragia fontium This patent atpD 334 Proteus mirabilis This patent atpD 335 Proteus vulgaris This patent atpD 336 Providencia alcalifaciens This patent atpD 337 Providencia rettgeri This patent atpD 338 Providencia rustigianii This patent atpD 339 Providencia stuartii This patent atpD 340 Psychrobacter phenylpyruvicum This patent atpD 341 Rahnella aquatilis This patent atpD 342 Salmonella choleraesuis subsp. arizonae This patent atpD 343 Salmonella choleraesuis subsp. choleraesuis This patent atpD serotype Choleraesuis 344 Salmonella choleraesuis subsp. diarizonae This patent atpD 345 Salmonella choleraesuis subsp. houtenae This patent atpD 346 Salmonella choleraesuis subsp. indica This patent atpD 347 Salmonella choleraesuis subsp. choleraesuis This patent atpD serotype Paratyphi A 348 Salmonella choleraesuis subsp. choleraesuis This patent atpD serotype Paratyphi B 349 Salmonella choleraesuis subsp. salamae This patent atpD 350 Salmonella choleraesuis subsp. choleraesuis serotype Typhi This patent atpD 351 Salmonella choleraesuis subsp. choleraesuis This patent atpD serotype Typhimurium 352 Salmonella choleraesuis subsp. choleraesuis This patent atpD serotype Virchow 353 Serratia ficaria This patent atpD 354 Serratia fonticola This patent atpD 355 Serratia grimesii This patent atpD 356 Serratia liquefaciens This patent atpD 357 Serratia marcescens This patent atpD 358 Serratia odorifera This patent atpD 359 Serratia plymuthica This patent atpD 360 Serratia rubidaea This patent atpD 361 Pseudomonas putida This patent atpD 362 Shigella boydii This patent atpD 363 Shigella dysenteriae This patent atpD 364 Shigella flexneri This patent atpD 365 Shigella sonnei This patent atpD 366 Staphylococcus aureus This patent atpD 367 Staphylococcus auricularis This patent atpD 368 Staphylococcus capitis subsp. capitis This patent atpD 369 Staphylococcus cohnii subsp. cohnii This patent atpD 370 Staphylococcus epidermidis This patent atpD 371 Staphylococcus haemolyticus This patent atpD 372 Staphylococcus hominis subsp. hominis This patent atpD 373 Staphylococcus hominis This patent atpD 374 Staphylococcus lugdunensis This patent atpD 375 Staphylococcus saprophyticus This patent atpD 376 Staphylococcus simulans This patent atpD 377 Staphylococcus wameri This patent atpD 378 Streptococcus acidominimus This patent atpD 379 Streptococcus agalactiae This patent atpD 380 Streptococcus agalactiae This patent atpD 381 Streptococcus agalactiae This patent atpD 382 Streptococcus agalactiae This patent atpD 383 Streptococcus agalactiae This patent atpD 384 Streptococcus dysgalactiae This patent atpD 385 Streptococcus equi subsp. equi This patent atpD 386 Streptococcus anginosus This patent atpD 387 Streptococcus salivarius This patent atpD 388 Streptococcus suis This patent atpD 389 Streptococcus uberis This patent atpD 390 Tatumella ptyseos This patent atpD 391 Trabulsiella guamensis This patent atpD 392 Yersinia bercovieri This patent atpD 393 Yersinia enterocolitica This patent atpD 394 Yersinia frederiksenii This patent atpD 395 Yersinia intermedia This patent atpD 396 Yersinia pseudotuberculosis This patent atpD 397 Yersinia rohdei This patent atpD 398 Yokenella regensburgei This patent atpD 399 Yarrowia lipolytica This patent tuf (EF-1) 400 Absidia corymbifera This patent tuf (EF-1) 401 Alternaria alternata This patent tuf (EF-1) 402 Aspergillus flavus This patent tuf (EF-1) 403 Aspergillus fumigatus This patent tuf (EF-1) 404 Aspergillus fumigatus This patent tuf (EF-1) 405 Aspergillus niger This patent tuf (EF-1) 406 Blastoschizomyces capitatus This patent tuf (EF-1) 407 Candida albicans This patent tuf (EF-1) 408 Candida albicans This patent tuf (EF-1) 409 Candida albicans This patent tuf (EF-1) 410 Candida albicans This patent tuf (EF-1) 411 Candida albicans This patent tuf (EF-1) 412 Candida dubliniensis This patent tuf (EF-1) 413 Candida catenulata This patent tuf (EF-1) 414 Candida dubliniensis This patent tuf (EF-1) 415 Candida dubliniensis This patent tuf (EF-1) 416 Candida famata This patent tuf (EF-1) 417 Candida glabrata WO98/20157 tuf (EF-1) 418 Candida guilliermondii This patent tuf (EF-1) 419 Candida haemulonii This patent tuf (EF-1) 420 Candida inconspicua This patent tuf (EF-1) 421 Candida kefyr This patent tuf (EF-1) 422 Candida krusei WO98/20157 tuf (EF-1) 423 Candida lambica This patent tuf (EF-1) 424 Candida lusitaniae This patent tuf (EF-1) 425 Candida norvegensis This patent tuf (EF-1) 426 Candida parapsilosis WO98/20157 tuf (EF-1) 427 Candida rugosa This patent tuf (EF-1) 428 Candida sphaerica This patent tuf (EF-1) 429 Candida tropicalis WO98/20157 tuf (EF-1) 430 Candida utilis This patent tuf (EF-1) 431 Candida viswanathii This patent tuf (EF-1) 432 Candida zeylanoides This patent tuf (EF-1) 433 Coccidioides immitis This patent tuf (EF-1) 434 Cryptococcus albidus This patent tuf (EF-1) 435 Exophiala jeanselmei This patent tuf (EF-1) 436 Fusarium oxysporum This patent tuf (EF-1) 437 Geotrichum sp. This patent tuf (EF-1) 438 Histoplasma capsulatum This patent tuf (EF-1) 439 Issatchenkia orientalis Kudrjanzev This patent tuf (EF-1) 440 Malassezia furfur This patent tuf (EF-1) 441 Malassezia pachydermatis This patent tuf (EF-1) 442 Malbranchea filamentosa This patent tuf (EF-1) 443 Metschnikowia pulcherrima This patent tuf (EF-1) 444 Paecilomyces lilacinus This patent tuf (EF-1) 445 Paracoccidioides brasiliensis This patent tuf (EF-1) 446 Penicillium marneffei This patent tuf (EF-1) 447 Pichia anomala This patent tuf (EF-1) 448 Pichia anomala This patent tuf (EF-1) 449 Pseudallescheria boydii This patent tuf (EF-1) 450 Rhizopus oryzae This patent tuf (EF-1) 451 Rhodotorula minuta This patent tuf (EF-1) 452 Sporobolomyces salmonicolor This patent tuf (EF-1) 453 Sporothrix schenckii This patent tuf (EF-1) 454 Stephanoascus ciferrii This patent tuf (EF-1) 455 Trichophyton mentagrophytes This patent tuf (EF-1) 456 Trichosporon cutaneum This patent tuf (EF-1) 457 Wangiella dermatitidis This patent tuf (EF-1) 458 Aspergillus fumigatus This patent atpD 459 Blastoschizomyces capitatus This patent atpD 460 Candida albicans This patent atpD 461 Candida dubliniensis This patent atpD 462 Candida famata This patent atpD 463 Candida glabrata This patent atpD 464 Candida guilliermondii This patent atpD 465 Candida haemulonii This patent atpD 466 Candida inconspicua This patent atpD 467 Candida kefyr This patent atpD 468 Candida krusei This patent atpD 469 Candida lambica This patent atpD 470 Candida lusitaniae This patent atpD 471 Candida norvegensis This patent atpD 472 Candida parapsilosis This patent atpD 473 Candida rugosa This patent atpD 474 Candida sphaerica This patent atpD 475 Candida tropicalis This patent atpD 476 Candida utilis This patent atpD 477 Candida viswanathii This patent atpD 478 Candida zeylanoides This patent atpD 479 Coccidioides immitis This patent atpD 480 Cryptococcus albidus This patent atpD 481 Fusarium oxysporum This patent atpD 482 Geotrichum sp. This patent atpD 483 Histoplasma capsulatum This patent atpD 484 Malassezia furfur This patent atpD 485 Malassezia pachydermatis This patent atpD 486 Metschnikowia pulcherrima This patent atpD 487 Penicillium mameffei This patent atpD 488 Pichia anomala This patent atpD 489 Pichia anomala This patent atpD 490 Rhodotorula minuta This patent atpD 491 Rhodotorula mucilaginosa This patent atpD 492 Sporobolomyces salmonicolor This patent atpD 493 Sporothrix schenckii This patent atpD 494 Stephanoascus ciferrii This patent atpD 495 Trichophyton mentagrophytes This patent atpD 496 Wangiella dermatitidis This patent atpD 497 Yarrowia lipolytica This patent atpD 498 Aspergillus fumigatus This patent tuf (M) 499 Blastoschizomyces capitatus This patent tuf (M) 500 Candida rugosa This patent tuf (M) 501 Coccidioides immitis This patent tuf (M) 502 Fusarium oxysporum This patent tuf (M) 503 Histoplasma capsulatum This patent tuf (M) 504 Paracoccidioides brasiliensis This patent tuf (M) 505 Penicillium marneffei This patent tuf (M) 506 Pichia anomala This patent tuf (M) 507 Trichophyton mentagrophytes This patent tuf (M) 508 Yarrowia lipolytica This patent tuf (M) 509 Babesia bigemina This patent tuf (EF-1) 510 Babesia bovis This patent tuf (EF-1) 511 Crithidia fasciculata This patent tuf (EF-1) 512 Entamoeba histolytica This patent tuf (EF-1) 513 Giardia lamblia This patent tuf (EF-1) 514 Leishmania tropica This patent tuf (EF-1) 515 Leishmania aethiopica This patent tuf (EF-1) 516 Leishmania tropica This patent tuf (EF-1) 517 Leishmania donovani This patent tuf (EF-1) 518 Leishmania infantum This patent tuf (EF-1) 519 Leishmania enriettii This patent tuf (EF-1) 520 Leishmania gerbilli This patent tuf (EF-1) 521 Leishmania hertigi This patent tuf (EF-1) 522 Leishmania major This patent tuf (EF-1) 523 Leishmania amazonensis This patent tuf (EF-1) 524 Leishmania mexicana This patent tuf (EF-1) 525 Leishmania tarentolae This patent tuf (EF-1) 526 Leishmania tropica This patent tuf (EF-1) 527 Neospora caninum This patent tuf (EF-1) 528 Trichomonas vaginalis This patent tuf (EF-1) 529 Trypanosoma brucei subsp. brucei This patent tuf (EF-1) 530 Crithidia fasciculata This patent atpD 531 Leishmania tropica This patent atpD 532 Leishmania aethiopica This patent atpD 533 Leishmania donovani This patent atpD 534 Leishmania infantum This patent atpD 535 Leishmania gerbilli This patent atpD 536 Leishmania hertigi This patent atpD 537 Leishmania major This patent atpD 538 Leishmania amazonensis This patent atpD 607 Enterococcus faecalis WO98/20157 tuf 608 Enterococcus faecium WO98/20157 tuf 609 Enterococcus gallinarum WO98/20157 tuf 610 Haemophilus influenzae WO98/20157 tuf 611 Staphylococcus epidermidis WO98/20157 tuf 612 Salmonella choleraesuis subsp. choleraesuis This patent tuf serotype Paratyphi A 613 Serratia ficaria This patent tuf 614 Enterococcus malodoratus This patent tuf (C) 615 Enterococcus durans This patent tuf (C) 616 Enterococcus pseudoavium This patent tuf (C) 617 Enterococcus dispar This patent tuf (C) 618 Enterococcus avium This patent tuf (C) 619 Saccharomyces cerevisiae Database tuf (M) 621 Enterococcus faecium This patent tuf (C) 622 Saccharomyces cerevisiae This patent tuf (EF-1) 623 Cryptococcus neoformans This patent tuf (EF-1) 624 Candida albicans WO98/20157 tuf (EF-1) 662 Corynebacterium diphtheriae WO98/20157 tuf 663 Candida catenulata This patent atpD 665 Saccharomyces cerevisiae Database tuf (EF-1) 666 Saccharomyces cerevisiae Database atpD 667 Trypanosoma cruzi This patent atpD 668 Corynebacterium glutamicum Database tuf 669 Escherichia coli Database atpD 670 Helicobacter pylori Database atpD 671 Clostridium acetobutylicum Database atpD 672 Cytophaga lytica Database atpD 673 Ehrlichia risticii This patent atpD 674 Vibrio cholerae This patent atpD 675 Vibrio cholerae This patent tuf 676 Leishmania enriettii This patent atpD 677 Babesia microti This patent tuf (EF-1) 678 Cryptococcus neoformans This patent atpD 679 Cryptococcus neoformans This patent atpD 680 Cunninghamella bertholletiae This patent atpD 684 Candida tropicalis Database atpD (V) 685 Enterococcus hirae Database atpD (V) 686 Chlamydia pneumoniae Database atpD (V) 687 Halobacterium salinarum Database atpD (V) 688 Homo sapiens Database atpD (V) 689 Plasmodium falciparum Database atpD (V) 690 Saccharomyces cerevisiae Database atpD (V) 691 Schizosaccharomyces pombe Database atpD (V) 692 Trypanosoma congolense Database atpD (V) 693 Thermus thermophilus Database atpD (V) 698 Escherichia coli WO98/20157 tuf 709 Borrelia burgdorferi Database atpD (V) 710 Treponema pallidum Database atpD (V) 711 Chlamydia trachomatis Genome project atpD (V) 712 Enterococcus faecalis Genome project atpD (V) 713 Methanosarcina barkeri Database atpD (V) 714 Methanococcus jannaschii Database atpD (V) 715 Porphyromonas gingivalis Genome project atpD (V) 716 Streptococcus pneumoniae Genome project atpD (V) 717 Burkholderia mallei This patent tuf 718 Burkholderia pseudomallei This patent tuf 719 Clostridium beijerinckii This patent tuf 720 Clostridium innocuum This patent tuf 721 Clostridium novyi This patent tuf 722 Clostridium septicum This patent tuf 723 Clostridium tertium This patent tuf 724 Clostridium tetani This patent tuf 725 Enterococcus malodoratus This patent tuf 726 Enterococcus sulfureus This patent tuf 727 Lactococcus garvieae This patent tuf 728 Mycoplasma pirum This patent tuf 729 Mycoplasma salivarium This patent tuf 730 Neisseria polysaccharea This patent tuf 731 Salmonella choleraesuis subsp. choleraesuis This patent tuf serotype Enteritidis 732 Salmonella choleraesuis subsp. choleraesuis This patent tuf serotype Gallinarum 733 Salmonella choleraesuis subsp. choleraesuis This patent tuf serotype Paratyphi B 734 Salmonella choleraesuis subsp. choleraesuis This patent tuf serotype Virchow 735 Serratia grimesii This patent tuf 736 Clostridium difficile This patent tuf 737 Burkholderia pseudomallei This patent atpD 738 Clostridium bifermentans This patent atpD 739 Clostridium beijerinckii This patent atpD 740 Clostridium difficile This patent atpD 741 Clostridium ramosum This patent atpD 742 Clostridium septicum This patent atpD 743 Clostridium tertium This patent atpD 744 Comamonas acidovorans This patent atpD 745 Klebsiella pneumoniae subsp. rhinoscleromatis This patent atpD 746 Neisseria canis This patent atpD 747 Neisseria cinerea This patent atpD 748 Neisseria cuniculi This patent atpD 749 Neisseria elongata subsp. elongata This patent atpD 750 Neisseria flavescens This patent atpD 751 Neisseria gonorrhoeae This patent atpD 752 Neisseria gonorrhoeae This patent atpD 753 Neisseria lactamica This patent atpD 754 Neisseria meningitidis This patent atpD 755 Neisseria mucosa This patent atpD 756 Neisseria subflava This patent atpD 757 Neisseria weaveri This patent atpD 758 Neisseria animalis This patent atpD 759 Proteus penneri This patent atpD 760 Salmonella choleraesuis subsp. choleraesuis This patent atpD serotype Enteritidis 761 Yersinia pestis This patent atpD 762 Burkholderia mallei This patent atpD 763 Clostridium sordellii This patent atpD 764 Clostridium novyi This patent atpD 765 Clostridium botulinum This patent atpD 766 Clostridium histolyticum This patent atpD 767 Peptostreptococcus prevotii This patent atpD 768 Absidia corymbifera This patent atpD 769 Alternaria alternata This patent atpD 770 Aspergillus flavus This patent atpD 771 Mucor circinelloides This patent atpD 772 Piedraia hortai This patent atpD 773 Pseudallescheria boydii This patent atpD 774 Rhizopus oryzae This patent atpD 775 Scopulariopsis koningii This patent atpD 776 Trichophyton mentagrophytes This patent atpD 777 Trichophyton tonsurans This patent atpD 778 Trichosporon cutaneum This patent atpD 779 Cladophialophora carrionii This patent tuf (EF-1) 780 Cunninghamella bertholletiae This patent tuf (EF-1) 781 Curvularia lunata This patent tuf (EF-1) 782 Fonsecaea pedrosoi This patent tuf (EF-1) 783 Microsporum audouinii This patent tuf (EF-1) 784 Mucor circinelloides This patent tuf (EF-1) 785 Phialophora verrucosa This patent tuf (EF-1) 786 Saksenaea vasiformis This patent tuf (EF-1) 787 Syncephalastrum racemosum This patent tuf (EF-1) 788 Trichophyton tonsurans This patent tuf (EF-1) 789 Trichophyton mentagrophytes This patent tuf (EF-1) 790 Bipolaris hawaiiensis This patent tuf (EF-1) 791 Aspergillus fumigatus This patent tuf (M) 792 Trichophyton mentagrophytes This patent tuf (M) 827 Clostridium novyi This patent atpD (V) 828 Clostridium difficile This patent atpD (V) 829 Clostridium septicum This patent atpD (V) 830 Clostridium botulinum This patent atpD (V) 831 Clostridium perfringens This patent atpD (V) 832 Clostridium tetani This patent atpD (V) 833 Streptococcus pyogenes Database atpD (V) 834 Babesia bovis This patent atpD (V) 835 Cryptosporidium parvum This patent atpD (V) 836 Leishmania infantum This patent atpD (V) 837 Leishmania major This patent atpD (V) 838 Leishmania tarentolae This patent atpD (V) 839 Trypanosoma brucei This patent atpD (V) 840 Trypanosoma cruzi This patent tuf (EF-1) 841 Trypanosoma cruzi This patent tuf (EF-1) 842 Trypanosoma cruzi This patent tuf (EF-1) 843 Babesia bovis This patent tuf (M) 844 Leishmania aethiopica This patent tuf (M) 845 Leishmania amazonensis This patent tuf (M) 846 Leishmania donovani This patent tuf (M) 847 Leishmania infantum This patent tuf (M) 848 Leishmania enriettii This patent tuf (M) 849 Leishmania gerbilli This patent tuf (M) 850 Leishmania major This patent tuf (M) 851 Leishmania mexicana This patent tuf (M) 852 Leishmania tarentolae This patent tuf (M) 853 Trypanosoma cruzi This patent tuf (M) 854 Trypanosoma cruzi This patent tuf (M) 855 Trypanosoma cruzi This patent tuf (M) 856 Babesia bigemina This patent atpD 857 Babesia bovis This patent atpD 858 Babesia microti This patent atpD 859 Leishmania guyanensis This patent atpD 860 Leishmania mexicana This patent atpD 861 Leishmania tropica This patent atpD 862 Leishmania tropica This patent atpD 863 Bordetella pertussis Database tuf 864 Trypanosoma brucei brucei Database tuf (EF-1) 865 Cryptosporidium parvum This patent tuf (EF-1) 866 Staphylococcus saprophyticus This patent atpD 867 Zoogloea ramigera This patent atpD 868 Staphylococcus saprophyticus This patent tuf 869 Enterococcus casseliflavus This patent tuf 870 Enterococcus casseliflavus This patent tuf 871 Enterococcus flavescens This patent tuf 872 Enterococcus gallinarum This patent tuf 873 Enterococcus gallinarum This patent tuf 874 Staphylococcus haemolyticus This patent tuf 875 Staphylococcus epidermidis This patent tuf 876 Staphylococcus epidermidis This patent tuf 877 Staphylococcus epidermidis This patent tuf 878 Staphylococcus epidermidis This patent tuf 879 Enterococcus gallinarum This patent tuf 880 Pseudomonas aeruginosa This patent tuf 881 Enterococcus casseliflavus This patent tuf 882 Enterococcus casseliflavus This patent tuf 883 Enterococcus faecalis This patent tuf 884 Enterococcus faecalis This patent tuf 885 Enterococcus faecium This patent tuf 886 Enterococcus faecium This patent tuf 887 Zoogloea ramigera This patent tuf 888 Enterococcus faecalis This patent tuf 889 Aspergillus fumigatus This patent atpD 890 Penicillium mameffei This patent atpD 891 Paecilomyces lilacinus This patent atpD 892 Penicillium mameffei This patent atpD 893 Sporothrix schenckii This patent atpD 894 Malbranchea filamentosa This patent atpD 895 Paecilomyces lilacinus This patent atpD 896 Aspergillus niger This patent atpD 897 Aspergillus fumigatus This patent tuf (EF-1) 898 Penicillium mameffei This patent tuf (EF-1) 899 Piedraia hortai This patent tuf (EF-1) 900 Paecilomyces lilacinus This patent tuf (EF-1) 901 Paracoccidioides brasiliensis This patent tuf (EF-1) 902 Sporothrix schenckii This patent tuf (EF-1) 903 Penicillium mameffei This patent tuf (EF-1) 904 Curvularia lunata This patent tuf (M) 905 Aspergillus niger This patent tuf (M) 906 Bipolaris hawaiiensis This patent tuf (M) 907 Aspergillus flavus This patent tuf (M) 908 Alternaria alternata This patent tuf (M) 909 Penicillium mameffei This patent tuf (M) 910 Penicillium mameffei This patent tuf (M) 918 Escherichia coli Database recA 929 Bacteroides fragilis This patent atpD (V) 930 Bacteroides distasonis This patent atpD (V) 931 Porphyromonas asaccharolytica This patent atpD (V) 932 Listeria monocytogenes This patent tuf 939 Saccharomyces cerevisiae Database recA (Rad51) 940 Saccharomyces cerevisiae Database recA (Dmc1) 941 Cryptococcus humicolus This patent atpD 942 Escherichia coli This patent atpD 943 Escherichia coli This patent atpD 944 Escherichia coli This patent atpD 945 Escherichia coli This patent atpD 946 Neisseria polysaccharea This patent atpD 947 Neisseria sicca This patent atpD 948 Streptococcus mitis This patent atpD 949 Streptococcus mitis This patent atpD 950 Streptococcus mitis This patent atpD 951 Streptococcus oralis This patent atpD 952 Streptococcus pneumoniae This patent atpD 953 Streptococcus pneumoniae This patent atpD 954 Streptococcus pneumoniae This patent atpD 955 Streptococcus pneumoniae This patent atpD 956 Babesia microti This patent atpD (V) 957 Entamoeba histolytica This patent atpD (V) 958 Fusobacterium nucleatum subsp. polymorphum This patent atpD (V) 959 Leishmania aethiopica This patent atpD (V) 960 Leishmania tropica This patent atpD (V) 961 Leishmania guyanensis This patent atpD (V) 962 Leishmania donovani This patent atpD (V) 963 Leishmania hertigi This patent atpD (V) 964 Leishmania mexicana This patent atpD (V) 965 Leishmania tropica This patent atpD (V) 966 Peptostreptococcus anaerobius This patent atpD (V) 967 Bordetella pertussis This patent tuf 968 Bordetella pertussis This patent tuf 969 Enterococcus columbae This patent tuf 970 Enterococcus flavescens This patent tuf 971 Streptococcus pneumoniae This patent tuf 972 Escherichia coli This patent tuf 973 Escherichia coli This patent tuf 974 Escherichia coli This patent tuf 975 Escherichia coli This patent tuf 976 Mycobacterium avium This patent tuf 977 Streptococcus pneumoniae This patent tuf 978 Mycobacterium gordonae This patent tuf 979 Streptococcus pneumoniae This patent tuf 980 Mycobacterium tuberculosis This patent tuf 981 Staphylococcus warneri This patent tuf 982 Streptococcus mitis This patent tuf 983 Streptococcus mitis This patent tuf 984 Streptococcus mitis This patent tuf 985 Streptococcus oralis This patent tuf 986 Streptococcus pneumoniae This patent tuf 987 Enterococcus hirae This patent tuf (C) 988 Enterococcus mundtii This patent tuf (C) 989 Enterococcus raffinosus This patent tuf (C) 990 Bacillus anthracis This patent recA 991 Prevotella melaninogenica This patent recA 992 Enterococcus casseliflavus This patent tuf 993 Streptococcus pyogenes Database speA 1002 Streptococcus pyogenes WO98/20157 tuf 1003 Bacillus cereus This patent recA 1004 Streptococcus pneumoniae This patent pbp1a 1005 Streptococcus pneumoniae This patent pbp1a 1006 Streptococcus pneumoniae This patent pbp1a 1007 Streptococcus pneumoniae This patent pbp1a 1008 Streptococcus pneumoniae This patent pbp1a 1009 Streptococcus pneumoniae This patent pbp1a 1010 Streptococcus pneumoniae This patent pbp1a 1011 Streptococcus pneumoniae This patent pbp1a 1012 Streptococcus pneumoniae This patent pbp1a 1013 Streptococcus pneumoniae This patent pbp1a 1014 Streptococcus pneumoniae This patent pbp1a 1015 Streptococcus pneumoniae This patent pbp1a 1016 Streptococcus pneumoniae This patent pbp1a 1017 Streptococcus pneumoniae This patent pbp1a 1018 Streptococcus pneumoniae This patent pbp1a 1019 Streptococcus pneumoniae This patent pbp2b 1020 Streptococcus pneumoniae This patent pbp2b 1021 Streptococcus pneumoniae This patent pbp2b 1022 Streptococcus pneumoniae This patent pbp2b 1023 Streptococcus pneumoniae This patent pbp2b 1024 Streptococcus pneumoniae This patent pbp2b 1025 Streptococcus pneumoniae This patent pbp2b 1026 Streptococcus pneumoniae This patent pbp2b 1027 Streptococcus pneumoniae This patent pbp2b 1028 Streptococcus pneumoniae This patent pbp2b 1029 Streptococcus pneumoniae This patent pbp2b 1030 Streptococcus pneumoniae This patent pbp2b 1031 Streptococcus pneumoniae This patent pbp2b 1032 Streptococcus pneumoniae This patent pbp2b 1033 Streptococcus pneumoniae This patent pbp2b 1034 Streptococcus pneumoniae This patent pbp2x 1035 Streptococcus pneumoniae This patent pbp2x 1036 Streptococcus pneumoniae This patent pbp2x 1037 Streptococcus pneumoniae This patent pbp2x 1038 Streptococcus pneumoniae This patent pbp2x 1039 Streptococcus pneumoniae This patent pbp2x 1040 Streptococcus pneumoniae This patent pbp2x 1041 Streptococcus pneumoniae This patent pbp2x 1042 Streptococcus pneumoniae This patent pbp2x 1043 Streptococcus pneumoniae This patent pbp2x 1044 Streptococcus pneumoniae This patent pbp2x 1045 Streptococcus pneumoniae This patent pbp2x 1046 Streptococcus pneumoniae This patent pbp2x 1047 Streptococcus pneumoniae This patent pbp2x 1048 Streptococcus pneumoniae This patent pbp2x 1049 Enterococcus faecium This patent vanA 1050 Enterococcus gallinarum This patent vanA 1051 Enterococcus faecium This patent vanA 1052 Enterococcus faecium This patent vanA 1053 Enterococcus faecium This patent vanA 1054 Enterococcus faecalis This patent vanA 1055 Enterococcus gallinarum This patent vanA 1056 Enterococcus faecium This patent vanA 1057 Enterococcus flavescens This patent vanA 1058 Enterococcus gallinarum This patent vanC1 1059 Enterococcus gallinarum This patent vanC1 1060 Enterococcus casseliflavus This patent vanC2 1061 Enterococcus casseliflavus This patent vanC2 1062 Enterococcus casseliflavus This patent vanC2 1063 Enterococcus casseliflavus This patent vanC2 1064 Enterococcus flavescens This patent vanC3 1065 Enterococcus flavescens This patent vanC3 1066 Enterococcus flavescens This patent vanC3 1067 Enterococcus faecium This patent vanXY 1068 Enterococcus faecium This patent vanXY 1069 Enterococcus faecium This patent vanXY 1070 Enterococcus faecalis This patent vanXY 1071 Enterococcus gallinarum This patent vanXY 1072 Enterococcus faecium This patent vanXY 1073 Enterococcus flavescens This patent vanXY 1074 Enterococcus faecium This patent vanXY 1075 Enterococcus gallinarum This patent vanXY 1076 Escherichia coli Database stx₁ 1077 Escherichia coli Database stx₂ 1093 Staphylococcus saprophyticus This patent unknown 1117 Enterococcus faecium Database vanB 1138 Enterococcus gallinarum Database vanC1 1139 Enterococcus faecium Database vanA 1140 Enterococcus casseliflavus Database vanC2 1141 Enterococcus faecium Database vanHAXY 1169 Streptococcus pneumoniae Database pbp1a 1172 Streptococcus pneumoniae Database pbp2b 1173 Streptococcus pneumoniae Database pbp2x 1178 Staphylococcus aureus Database mecA 1183 Streptococcus pneumoniae Database hexA 1184 Streptococcus pneumoniae This patent hexA 1185 Streptococcus pneumoniae This patent hexA 1186 Streptococcus pneumoniae This patent hexA 1187 Streptococcus pneumoniae This patent hexA 1188 Streptococcus oralis This patent hexA 1189 Streptococcus mitis This patent hexA 1190 Streptococcus mitis This patent hexA 1191 Streptococcus mitis This patent hexA 1198 Staphylococcus saprophyticus This patent unknown 1215 Streptococcus pyogenes Database pcp 1230 Escherichia coli Database tuf (EF-G) 1242 Enterococcus faecium Database ddl 1243 Enterococcus faecalis Database mtlF, mtlD 1244 Staphylococcus aureus subsp. aureus This patent unknown 1245 Bacillus anthracis This patent atpD 1246 Bacillus mycoides This patent atpD 1247 Bacillus thuringiensis This patent atpD 1248 Bacillus thuringiensis This patent atpD 1249 Bacillus thuringiensis This patent atpD 1250 Bacillus weihenstephanensis This patent atpD 1251 Bacillus thuringiensis This patent atpD 1252 Bacillus thuringiensis This patent atpD 1253 Bacillus cereus This patent atpD 1254 Bacillus cereus This patent atpD 1255 Staphylococcus aureus This patent gyrA 1256 Bacillus weihenstephanensis This patent atpD 1257 Bacillus anthracis This patent atpD 1258 Bacillus thuringiensis This patent atpD 1259 Bacillus cereus This patent atpD 1260 Bacillus cereus This patent atpD 1261 Bacillus thuringiensis This patent atpD 1262 Bacillus thuringiensis This patent atpD 1263 Bacillus thuringiensis This patent atpD 1264 Bacillus thuringiensis This patent atpD 1265 Bacillus anthracis This patent atpD 1266 Paracoccidioides brasiliensis This patent tuf (EF-1) 1267 Blastomyces dermatitidis This patent tuf (EF-1) 1268 Histoplasma capsulatum This patent tuf (EF-1) 1269 Trichophyton rubrum This patent tuf (EF-1) 1270 Microsporum canis This patent tuf (EF-1) 1271 Aspergillus versicolor This patent tuf (EF-1) 1272 Exophiala moniliae This patent tuf (EF-1) 1273 Hortaea wemeckii This patent tuf (EF-1) 1274 Fusarium solani This patent tuf (EF-1) 1275 Aureobasidium pullulans This patent tuf (EF-1) 1276 Blastomyces dermatitidis This patent tuf (EF-1) 1277 Exophiala dermatitidis This patent tuf (EF-1) 1278 Fusarium moniliforme This patent tuf (EF-1) 1279 Aspergillus terreus This patent tuf (EF-1) 1280 Aspergillus fumigatus This patent tuf (EF-1) 1281 Cryptococcus laurentii This patent tuf (EF-1) 1282 Emmonsia parva This patent tuf (EF-1) 1283 Fusarium solani This patent tuf (EF-1) 1284 Sporothrix schenckii This patent tuf (EF-1) 1285 Aspergillus nidulans This patent tuf (EF-1) 1286 Cladophialophora carrionii This patent tuf (EF-1) 1287 Exserohilum rostratum This patent tuf (EF-1) 1288 Bacillus thuringiensis This patent recA 1289 Bacillus thuringiensis This patent recA 1299 Staphylococcus aureus Database gyrA 1300 Escherichia coli Database gyrA 1307 Staphylococcus aureus Database gyrB 1320 Escherichia coli Database parC (grlA) 1321 Staphylococcus aureus Database parC (grlA) 1328 Staphylococcus aureus Database parE (grlB) 1348 unidentified bacterium Database aac2Ia 1351 Pseudomonas aeruginosa Database aac3Ib 1356 Serratia marcescens Database aac3IIb 1361 Escherichia coli Database aac3IVa 1366 Enterobacter cloacae Database aac3VIa 1371 Citrobacter koseri Database aac6Ia 1376 Serratia marcescens Database aac6Ic 1381 Escherichia coli Database ant3Ia 1386 Staphylococcus aureus Database ant4Ia 1391 Escherichia coli Database aph3Ia 1396 Escherichia coli Database aph3IIa 1401 Enterococcus faecalis Database aph3IIIa 1406 Acinetobacter baumannii Database aph3VIa 1411 Pseudomonas aeruginosa Database blaCARB 1416 Klebsiella pneumoniae Database blaCMY-2 1423 Escherichia coli Database blaCTX-M-1 1428 Salmonella choleraesuis subsp. choleraesuis serotype Database blaCTX-M-2 Typhimurium 1433 Pseudomonas aeruginosa Database blaIMP 1438 Escherichia coli Database blaOXA2 1439 Pseudomonas aeruginosa Database blaOXA10 1442 Pseudomonas aeruginosa Database blaPER1 1445 Salmonella choleraesuis subsp. choleraesuis serotype Database blaPER2 Typhimurium 1452 Staphylococcus epidermidis Database dfrA 1461 Escherichia coli Database dhfrIa 1470 Escherichia coli Database dhfrIb 1475 Escherichia coli Database dhfrV 1480 Proteus mirabilis Database dhfrVI 1489 Escherichia coli Database dhfrVII 1494 Escherichia coli Database dhfrVIII 1499 Escherichia coli Database dhfrIX 1504 Escherichia coli Database dhfrXII 1507 Escherichia coli Database dhfrXIII 1512 Escherichia coli Database dhfrXV 1517 Escherichia coli Database dhfrXVII 1518 Acinetobacter lwoffii This patent fusA 1519 Acinetobacter lwoffii This patent fusA-tuf spacer 1520 Acinetobacter lwoffii This patent tuf 1521 Haemophilus influenzae This patent fusA 1522 Haemophilus influenzae This patent fusA-tuf spacer 1523 Haemophilus influenzae This patent tuf 1524 Proteus mirabilis This patent fusA 1525 Proteus mirabilis This patent fusA-tuf spacer 1526 Proteus mirabilis This patent fuf 1527 Campylobacter curvus This patent atpD 1530 Escherichia coli Database ereA 1535 Escherichia coli Database ereB 1540 Staphylococcus haemolyticus Database linA 1545 Enterococcus faecium Database linB 1548 Streptococcus pyogenes Database mefA 1551 Streptococcus pneumoniae Database mefE 1560 Escherichia coli Database mphA 1561 Candida albicans This patent tuf (EF-1) 1562 Candida dubliniensis This patent tuf (EF-1) 1563 Candida famata This patent tuf (EF-1) 1564 Candida glabrata This patent tuf (EF-1) 1565 Candida guilliermondii This patent tuf (EF-1) 1566 Candida haemulonii This patent tuf (EF-1) 1567 Candida kefyr This patent tuf (EF-1) 1568 Candida lusitaniae This patent tuf (EF-1) 1569 Candida sphaerica This patent tuf (EF-1) 1570 Candida tropicalis This patent tuf (EF-1) 1571 Candida viswanathii This patent tuf (EF-1) 1572 Alcaligenes faecalis subsp. faecalis This patent tuf 1573 Prevotella buccalis This patent tuf 1574 Succinivibrio dextrinosolvens This patent tuf 1575 Tetragenococcus halophilus This patent tuf 1576 Campylobacter jejuni subsp. jejuni This patent atpD 1577 Campylobacter rectus This patent atpD 1578 Enterococcus casseliflavus This patent fusA 1579 Enterococcus gallinarum This patent fusA 1580 Streptococcus mitis This patent fusA 1585 Enterococcus faecium Database satG 1590 Cloning vector pFW16 Database tetM 1594 Enterococcus faecium Database vanD 1599 Enterococcus faecalis Database vanE 1600 Campylobacter jejuni subsp. doylei This patent atpD 1601 Enterococcus sulfurous This patent atpD 1602 Enterococcus solitarius This patent atpD 1603 Campylobacter sputorum subsp. sputorum This patent atpD 1604 Enterococcus pseudoavium This patent atpD 1607 Klebsiella omithinolytica This patent gyrA 1608 Klebsiella oxytoca This patent gyrA 1613 Staphylococcus aureus Database vatB 1618 Staphylococcus cohnii Database vatC 1623 Staphylococcus aureus Database vga 1628 Staphylococcus aureus Database vgaB 1633 Staphylococcus aureus Database vgb 1638 Aspergillus fumigatus This patent atpD 1639 Aspergillus fumigatus This patent atpD 1640 Bacillus mycoides This patent atpD 1641 Bacillus mycoides This patent atpD 1642 Bacillus mycoides This patent atpD 1643 Bacillus pseudomycoides This patent atpD 1644 Bacillus pseudomycoides This patent atpD 1645 Budvicia aquatica This patent atpD 1646 Buttiauxella agrestis This patent atpD 1647 Candida norvegica This patent atpD 1648 Streptococcus pneumoniae This patent pbp1a 1649 Campylobacter lari This patent atpD 1650 Coccidioides immitis This patent atpD 1651 Emmonsia parva This patent atpD 1652 Erwinia amylovora This patent atpD 1653 Fonsecaea pedrosoi This patent atpD 1654 Fusarium moniliforme This patent atpD 1655 Klebsiella oxytoca This patent atpD 1656 Microsporum audouinii This patent atpD 1657 Obesumbacterium proteus This patent atpD 1658 Paracoccidioides brasiliensis This patent atpD 1659 Plesiomonas shigelloides This patent atpD 1660 Shewanella putrefaciens This patent atpD 1662 Campylobacter curvus This patent tuf 1663 Campylobacter rectus This patent tuf 1664 Fonsecaea pedrosoi This patent tuf 1666 Microsporum audouinii This patent tuf 1667 Piedraia hortai This patent tuf 1668 Escherichia coli Database tuf 1669 Saksenaea vasiformis This patent tuf 1670 Trichophyton tonsurans This patent tuf 1671 Enterobacter aerogenes This patent atpD 1672 Bordetella pertussis Database atpD 1673 Arcanobacterium haemolyticum This patent tuf 1674 Butyrivibrio fibrisolvens This patent tuf 1675 Campylobacter jejuni subsp. doylei This patent tuf 1676 Campylobacter lari This patent tuf 1677 Campylobacter sputorum subsp. sputorum This patent tuf 1678 Campylobacter upsaliensis This patent tuf 1679 Globicatella sanguis This patent tuf 1680 Lactobacillus acidophilus This patent tuf 1681 Leuconostoc mesenteroides subsp. dextranicum This patent tuf 1682 Prevotella buccalis This patent tuf 1683 Ruminococcus bromii This patent tuf 1684 Paracoccidioides brasiliensis This patent atpD 1685 Candida norvegica This patent tuf (EF-1) 1686 Aspergillus nidulans This patent tuf 1687 Aspergillus terreus This patent tuf 1688 Candida norvegica This patent tuf 1689 Candida parapsilosis This patent tuf 1702 Streptococcus gordonii WO98/20157 recA 1703 Streptococcus mutans WO98/20157 recA 1704 Streptococcus pneumoniae WO98/20157 recA 1705 Streptococcus pyogenes WO98/20157 recA 1706 Streptococcus salivarius subsp. thermophilus WO98/20157 recA 1707 Escherichia coli WO98/20157 oxa 1708 Enterococcus faecalis WO98/20157 blaZ 1709 Pseudomonas aeruginosa WO98/20157 aac6′-IIa 1710 Staphylococcus aureus WO98/20157 ermA 1711 Escherichia coli WO98/20157 ermB 1712 Staphylococcus aureus WO98/20157 ermC 1713 Enterococcus faecalis WO98/20157 vanB 1714 Campylobacter jejuni subsp. jejuni This patent recA 1715 Abiotrophia adiacens WO98/20157 tuf 1716 Abiotrophia defectiva WO98/20157 tuf 1717 Corynebacterium accolens WO98/20157 tuf 1718 Corynebacterium genitalium WO98/20157 tuf 1719 Corynebacterium jeikeium WO98/20157 tuf 1720 Corynebacterium pseudodiphtheriticum WO98/20157 tuf 1721 Corynebacterium striatum WO98/20157 tuf 1722 Enterococcus avium WO98/20157 tuf 1723 Gardnerella vaginalis WO98/20157 tuf 1724 Listeria innocua WO98/20157 tuf 1725 Listeria ivanovii WO98/20157 tuf 1726 Listeria monocytogenes WO98/20157 tuf 1727 Listeria seeligeri WO98/20157 tuf 1728 Staphylococcus aureus WO98/20157 tuf 1729 Staphylococcus saprophyticus WO98/20157 tuf 1730 Staphylococcus simulans WO98/20157 tuf 1731 Streptococcus agalactiae WO98/20157 tuf 1732 Streptococcus pneumoniae WO98/20157 tuf 1733 Streptococcus salivarius WO98/20157 tuf 1734 Agrobacterium radiobacter WO98/20157 tuf 1735 Bacillus subtilis WO98/20157 tuf 1736 Bacteroides fragilis WO98/20157 tuf 1737 Borrelia burgdorferi WO98/20157 tuf 1738 Brevibacterium linens WO98/20157 tuf 1739 Chlamydia trachomatis WO98/20157 tuf 1740 Fibrobacter succinogenes WO98/20157 tuf 1741 Flavobacterium ferrugineum WO98/20157 tuf 1742 Helicobacter pylori WO98/20157 tuf 1743 Micrococcus luteus WO98/20157 tuf 1744 Mycobacterium tuberculosis WO98/20157 tuf 1745 Mycoplasma genitalium WO98/20157 tuf 1746 Neisseria gonorrhoeae WO98/20157 tuf 1747 Rickettsia prowazekii WO98/20157 tuf 1748 Salmonella choleraesuis subsp. choleraesuis WO98/20157 tuf serotype Typhimurium 1749 Shewanella putrefaciens WO98/20157 tuf 1750 Stigmatella aurantiaca WO98/20157 tuf 1751 Thiomonas cuprina WO98/20157 tuf 1752 Treponema pallidum WO98/20157 tuf 1753 Ureaplasma urealyticum WO98/20157 tuf 1754 Wolinella succinogenes WO98/20157 tuf 1755 Burkholderia cepacia WO98/20157 tuf 1756 Bacillus anthracis This patent recA 1757 Bacillus anthracis This patent recA 1758 Bacillus cereus This patent recA 1759 Bacillus cereus This patent recA 1760 Bacillus mycoides This patent recA 1761 Bacillus pseudomycoides This patent recA 1762 Bacillus thuringiensis This patent recA 1763 Bacillus thuringiensis This patent recA 1764 Klebsiella oxytoca This patent gyrA 1765 Klebsiella pneumoniae subsp. ozaenae This patent gyrA 1766 Klebsiella planticola This patent gyrA 1767 Klebsiella pneumoniae This patent gyrA 1768 Klebsiella pneumoniae subsp. pneumoniae This patent gyrA 1769 Klebsiella pneumoniae subsp. pneumoniae This patent gyrA 1770 Klebsiella pneumoniae subsp. rhinoscleromatis This patent gyrA 1771 Klebsiella terrigena This patent gyrA 1772 Legionella pneumophila subsp. pneumophila This patent gyrA 1773 Proteus mirabilis This patent gyrA 1774 Providencia rettgeri This patent gyrA 1775 Proteus vulgaris This patent gyrA 1776 Yersinia enterocolitica This patent gyrA 1777 Klebsiella oxytoca This patent parC (grlA) 1778 Klebsiella oxytoca This patent parC (grlA) 1779 Klebsiella pneumoniae subsp. ozaenae This patent parC (grlA) 1780 Klebsiella planticola This patent parC (grlA) 1781 Klebsiella pneumoniae This patent parC (grlA) 1782 Klebsiella pneumoniae subsp. pneumoniae This patent parC (grlA) 1783 Klebsiella pneumoniae subsp. pneumoniae This patent parC (grlA) 1784 Klebsiella pneumoniae subsp. rhinoscleromatis This patent parC (grlA) 1785 Klebsiella terrigena This patent parC (grlA) 1786 Bacillus cereus This patent fusA 1787 Bacillus cereus This patent fusA 1788 Bacillus anthracis This patent fusA 1789 Bacillus cereus This patent fusA 1790 Bacillus anthracis This patent fusA 1791 Bacillus pseudomycoides This patent fusA 1792 Bacillus cereus This patent fusA 1793 Bacillus anthracis This patent fusA 1794 Bacillus cereus This patent fusA 1795 Bacillus weihenstephanensis This patent fusA 1796 Bacillus mycoides This patent fusA 1797 Bacillus thuringiensis This patent fusA 1798 Bacillus weihenstephanensis This patent fusA-tuf spacer 1799 Bacillus thuringiensis This patent fusA-tuf spacer 1800 Bacillus anthracis This patent fusA-tuf spacer 1801 Bacillus pseudomycoides This patent fusA-tuf spacer 1802 Bacillus anthracis This patent fusA-tuf spacer 1803 Bacillus cereus This patent fusA-tuf spacer 1804 Bacillus cereus This patent fusA-tuf spacer 1805 Bacillus mycoides This patent fusA-tuf spacer 1806 Bacillus cereus This patent fusA-tuf spacer 1807 Bacillus cereus This patent fusA-tuf spacer 1808 Bacillus cereus This patent fusA-tuf spacer 1809 Bacillus anthracis This patent fusA-tuf spacer 1810 Bacillus mycoides This patent tuf 1811 Bacillus thuringiensis This patent tuf 1812 Bacillus cereus This patent tuf 1813 Bacillus weihenstephanensis This patent tuf 1814 Bacillus anthracis This patent tuf 1815 Bacillus cereus This patent tuf 1816 Bacillus cereus This patent tuf 1817 Bacillus anthracis This patent tuf 1818 Bacillus cereus This patent tuf 1819 Bacillus anthracis This patent tuf 1820 Bacillus pseudomycoides This patent tuf 1821 Bacillus cereus This patent tuf 1822 Streptococcus oralis This patent fusA 1823 Budvicia aquatica This patent fusA 1824 Buttiauxella agrestis This patent fusA 1825 Klebsiella oxytoca This patent fusA 1826 Plesiomonas shigelloides This patent fusA 1827 Shewanella putrefaciens This patent fusA 1828 Obesumbacterium proteus This patent fusA 1829 Klebsiella oxytoca This patent fusA-tuf spacer 1830 Budvicia aquatica This patent fusA-tuf spacer 1831 Plesiomonas shigelloides This patent fusA-tuf spacer 1832 Obesumbacterium proteus This patent fusA-tuf spacer 1833 Shewanella putrefaciens This patent fusA-tuf spacer 1834 Buttiauxella agrestis This patent fusA-tuf spacer 1835 Campylobacter coli This patent tuf 1836 Campylobacter fetus subsp. fetus This patent tuf 1837 Campylobacter fetus subsp. venerealis This patent tuf 1838 Buttiauxella agrestis This patent tuf 1839 Klebsiella oxytoca This patent tuf 1840 Plesiomonas shigelloides This patent tuf 1841 Shewanella putrefaciens This patent tuf 1842 Obesumbacterium proteus This patent tuf 1843 Budvicia aquatica This patent tuf 1844 Abiotrophia adiacens This patent atpD 1845 Arcanobacterium haemolyticum This patent atpD 1846 Basidiobolus ranarum This patent atpD 1847 Blastomyces dermatitidis This patent atpD 1848 Blastomyces dermatitidis This patent atpD 1849 Campylobacter coli This patent atpD 1850 Campylobacter fetus subsp. fetus This patent atpD 1851 Campylobacter fetus subsp. venerealis This patent atpD 1852 Campylobacter gracilis This patent atpD 1853 Campylobacter jejuni subsp. jejuni This patent atpD 1854 Enterococcus cecorum This patent atpD 1855 Enterococcus columbae This patent atpD 1856 Enterococcus dispar This patent atpD 1857 Enterococcus malodoratus This patent atpD 1858 Enterococcus mundtii This patent atpD 1859 Enterococcus raffinosus This patent atpD 1860 Globicatella sanguis This patent atpD 1861 Lactococcus garvieae This patent atpD 1862 Lactococcus lactis This patent atpD 1863 Listeria ivanovii This patent atpD 1864 Succinivibrio dextrinosolvens This patent atpD 1865 Tetragenococcus halophilus This patent atpD 1866 Campylobacter fetus subsp. fetus This patent recA 1867 Campylobacter fetus subsp. venerealis This patent recA 1868 Campylobacter jejuni subsp. jejuni This patent recA 1869 Enterococcus avium This patent recA 1870 Enterococcus faecium This patent recA 1871 Listeria monocytogenes This patent recA 1872 Streptococcus mitis This patent recA 1873 Streptococcus oralis This patent recA 1874 Aspergillus fumigatus This patent tuf (M) 1875 Aspergillus versicolor This patent tuf (M) 1876 Basidiobolus ranarum This patent tuf (M) 1877 Campylobacter gracilis This patent tuf 1878 Campylobacter jejuni subsp. jejuni This patent tuf 1879 Coccidioides immitis This patent tuf (M) 1880 Erwinia amylovora This patent tuf 1881 Salmonella choleraesuis subsp. choleraesuis serotype This patent tuf Typhimurium 1899 Klebsiella pneumoniae Database blaSHV 1900 Klebsiella pneumoniae Database blaSHV 1901 Escherichia coli Database blaSHV 1902 Klebsiella pneumoniae Database blaSHV 1903 Klebsiella pneumoniae Database blaSHV 1904 Escherichia coli Database blaSHV 1905 Pseudomonas aeruginosa Database blaSHV 1927 Neisseria meningitidis Database blaTEM 1928 Escherichia coli Database blaTEM 1929 Klebsiella oxytoca Database blaTEM 1930 Escherichia coli Database blaTEM 1931 Escherichia coli Database blaTEM 1932 Escherichia coli Database blaTEM 1933 Escherichia coli Database blaTEM 1954 Klebsiella pneumoniae subsp. pneumoniae Database gyrA 1956 Candida inconspicua This patent tuf (M) 1957 Candida utilis This patent tuf (M) 1958 Candida zeylanoides This patent tuf (M) 1959 Candida catenulata This patent tuf (M) 1960 Candida krusei This patent tuf (M) 1965 Plasmid pGS05 Database sulII 1970 Transposon Tn10 Database tetB 1985 Cryptococcus neoformans Database tuf (EF-1) 1986 Cryptococcus neoformans Database tuf (EF-1) 1987 Saccharomyces cerevisiae Database tuf (EF-1) 1988 Saccharomyces cerevisiae Database tuf (EF-1) 1989 Eremothecium gossypii Database tuf (EF-1) 1990 Eremothecium gossypii Database tuf (EF-1) 1991 Aspergillus oryzae Database tuf (EF-1) 1992 Aureobasidium pullulans Database tuf (EF-1) 1993 Histoplasma capsulatum Database tuf (EF-1) 1994 Neurospora crassa Database tuf (EF-1) 1995 Podospora anserina Database tuf (EF-1) 1996 Podospora curvicolla Database tuf (EF-1) 1997 Sordaria macrospora Database tuf (EF-1) 1998 Trichoderma reesei Database tuf (EF-1) 2004 Candida albicans Database tuf (M) 2005 Schizosaccharomyces pombe Database tuf (M) 2010 Klebsiella pneumoniae Database blaTEM 2011 Klebsiella pneumoniae Database blaTEM 2013 Kluyvera ascorbata This patent gyrA 2014 Kluyvera georgiana This patent gyrA 2047 Streptococcus pneumoniae Database pbp1A 2048 Streptococcus pneumoniae Database pbp1A 2049 Streptococcus pneumoniae Database pbp1A 2050 Streptococcus pneumoniae Database pbp1A 2051 Streptococcus pneumoniae Database pbp1A 2052 Streptococcus pneumoniae Database pbp1A 2053 Streptococcus pneumoniae Database pbp1A 2054 Streptococcus pneumoniae Database gyrA 2055 Streptococcus pneumoniae Database parC 2056 Streptococcus pneumoniae This patent pbp1A 2057 Streptococcus pneumoniae This patent pbp1A 2058 Streptococcus pneumoniae This patent pbp1A 2059 Streptococcus pneumoniae This patent pbp1A 2060 Streptococcus pneumoniae This patent pbp1A 2061 Streptococcus pneumoniae This patent pbp1A 2062 Streptococcus pneumoniae This patent pbp1A 2063 Streptococcus pneumoniae This patent pbp1A 2064 Streptococcus pneumoniae This patent pbp1A 2072 Mycobacterium tuberculosis Database rpoB 2097 Mycoplasma pneumoniae Database tuf 2101 Mycobacterium tuberculosis Database inhA 2105 Mycobacterium tuberculosis Database embB 2129 Clostridium difficile Database cdtA 2130 Clostridium difficile Database cdtB 2137 Pseudomonas putida Genome project tuf 2138 Pseudomonas aeruginosa Genome project tuf 2139 Campylobacter jejuni Database atpD 2140 Streptococcus pneumoniae Database pbp1a 2144 Staphylococcus aureus Database mupA 2147 Escherichia coli Database catI 2150 Escherichia coli Database catII 2153 Shigella flexneri Database catIII 2156 Clostridium perfringens Database catP 2159 Staphylococcus aureus Database cat 2162 Staphylococcus aureus Database cat 2165 Salmonella typhimurium Database ppflo-like 2183 Alcaligenes faecalis subsp. faecalis This patent tuf 2184 Campylobacter coli This patent fusA 2185 Succinivibrio dextrinosolvens This patent tuf 2186 Tetragenococcus halophilus This patent tuf 2187 Campylobacter jejuni subsp. jejuni This patent fusA 2188 Campylobacter jejuni subsp. jejuni This patent fusA 2189 Leishmania guyanensis This patent atpD 2190 Trypanosoma brucei brucei This patent atpD 2191 Aspergillus nidulans This patent atpD 2192 Leishmania panamensis This patent atpD 2193 Aspergillus nidulans This patent tuf (M) 2194 Aureobasidium pullulans This patent tuf (M) 2195 Emmonsia parva This patent tuf (M) 2196 Exserohilum rostratum This patent tuf (M) 2197 Fusarium moniliforme This patent tuf (M) 2198 Fusarium solani This patent tuf (M) 2199 Histoplasma capsulatum This patent tuf (M) 2200 Kocuria kristinae This patent tuf 2201 Vibrio mimicus This patent tuf 2202 Citrobacter freundii This patent recA 2203 Clostridium botulinum This patent recA 2204 Francisella tularensis This patent recA 2205 Peptostreptococcus anaerobius This patent recA 2206 Peptostreptococcus asaccharolyticus This patent recA 2207 Providencia stuartii This patent recA 2208 Salmonella choleraesuis subsp. choleraesuis This patent recA serotype Paratyphi A 2209 Salmonella choleraesuis subsp. choleraesuis This patent recA serotype Typhimurium 2210 Staphylococcus saprophyticus This patent recA 2211 Yersinia pseudotuberculosis This patent recA 2212 Zoogloea ramigera This patent recA 2214 Abiotrophia adiacens This patent fusA 2215 Acinetobacter baumannii This patent fusA 2216 Actinomyces meyeri This patent fusA 2217 Clostridium difficile This patent fusA 2218 Corynebacterium diphtheriae This patent fusA 2219 Enterobacter cloacae This patent fusA 2220 Klebsiella pneumoniae subsp. pneumoniae This patent fusA 2221 Listeria monocytogenes This patent fusA 2222 Mycobacterium avium This patent fusA 2223 Mycobacterium gordonae This patent fusA 2224 Mycobacterium kansasii This patent fusA 2225 Mycobacterium terrae This patent fusA 2226 Neisseria polysaccharea This patent fusA 2227 Staphylococcus epidermidis This patent fusA 2228 Staphylococcus haemolyticus This patent fusA 2229 Succinivibrio dextrinosolvens This patent fusA 2230 Tetragenococcus halophilus This patent fusA 2231 Veillonella parvula This patent fusA 2232 Yersinia pseudotuberculosis This patent fusA 2233 Zoogloea ramigera This patent fusA 2234 Aeromonas hydrophila This patent fusA 2235 Abiotrophia adiacens This patent fusA-tuf spacer 2236 Acinetobacter baumannii This patent fusA-tuf spacer 2237 Actinomyces meyeri This patent fusA-tuf spacer 2238 Clostridium difficile This patent fusA-tuf spacer 2239 Corynebacterium diphtheriae This patent fusA-tuf spacer 2240 Enterobacter cloacae This patent fusA-tuf spacer 2241 Klebsiella pneumoniae subsp. pneumoniae This patent fusA-tuf spacer 2242 Listeria monocytogenes This patent fusA-tuf spacer 2243 Mycobacterium avium This patent fusA-tuf spacer 2244 Mycobacterium gordonae This patent fusA-tuf spacer 2245 Mycobacterium kansasii This patent fusA-tuf spacer 2246 Mycobacterium terrae This patent fusA-tuf spacer 2247 Neisseria polysaccharea This patent fusA-tuf spacer 2248 Staphylococcus epidermidis This patent fusA-tuf spacer 2249 Staphylococcus haemolyticus This patent fusA-tuf spacer 2255 Abiotrophia adiacens This patent tuf 2256 Acinetobacter baumannii This patent tuf 2257 Actinomyces meyeri This patent tuf 2258 Clostridium difficile This patent tuf 2259 Corynebacterium diphtheriae This patent tuf 2260 Enterobacter cloacae This patent tuf 2261 Klebsiella pneumoniae subsp. pneumoniae This patent tuf 2262 Listeria monocytogenes This patent tuf 2263 Mycobacterium avium This patent tuf 2264 Mycobacterium gordonae This patent tuf 2265 Mycobacterium kansasii This patent tuf 2266 Mycobacterium terrae This patent tuf 2267 Neisseria polysaccharea This patent tuf 2268 Staphylococcus epidermidis This patent tuf 2269 Staphylococcus haemolyticus This patent tuf 2270 Aeromonas hydrophila This patent tuf 2271 Bilophila wadsworthia This patent tuf 2272 Brevundimonas diminuta This patent tuf 2273 Streptococcus mitis This patent pbp1a 2274 Streptococcus mitis This patent pbp1a 2275 Streptococcus mitis This patent pbp1a 2276 Streptococcus oralis This patent pbp1a 2277 Escherichia coli This patent gyrA 2278 Escherichia coli This patent gyrA 2279 Escherichia coli This patent gyrA 2280 Escherichia coli This patent gyrA 2288 Enterococcus faecium Database ddl 2293 Enterococcus faecium Database vanA 2296 Enterococcus faecalis Database vanB *tuf indicates tuf sequences, tuf (C) indicates tuf sequences divergent from main (usually A and B) copies of the elongation factor-Tu, tuf (EF-1) indicates tuf sequences of the eukaryotic type (elongation factor 1α), tuf (M) indicates tuf sequences from organellar (mostly mitochondrial) origin. fusA indicates fusA sequences; fusA-tuf spacer indicates the intergenic region between fusA and tuf. atpD indicates atpD sequences of the F-type, atpD (V) indicates atpD sequences of the V-type. recA indicates recA sequences, recA(Rad51) indicates rad51 sequences or homologs and recA(Dmc1) indicates dmc1 sequences or homologs.

TABLE 8 Bacterial species used to test the specificity of the Streptococcus agalactiae-specific amplification primers derived from tuf sequences. Strain Reference number Strain Reference number Streptococcus acidominimus ATCC 51726 Bacteroides caccae ATCC 43185 Streptococcus agalactiae ATCC 12403 Bacteroides vulgatus ATCC 8482 Streptococcus agalactiae ATCC 12973 Bacteroides fragilis ATCC 25285 Streptococcus agalactiae ATCC 13813 Candida albicans ATCC 11006 Streptococcus agalactiae ATCC 27591 Clostridium innoculum ATCC 14501 Streptococcus agalactiae CDCs 1073 Clostridium ramosum ATCC 25582 Streptococcus anginosus ATCC 27335 Lactobacillus casei subsp. casei ATCC 393 Streptococcus anginosus ATCC 33397 Clostridium septicum ATCC 12464 Streptococcus bovis ATCC 33317 Corynebacterium cervicis NCTC 10604 Streptococcus anginosus ATCC 27823 Corynebacterium genitalium ATCC 33031 Streptococcus cricetus ATCC 19642 Corynebacterium urealyticum ATCC 43042 Streptococcus cristatus ATCC 51100 Enterococcus faecalis ATCC 29212 Streptococcus downei ATCC 33748 Enterococcus faecium ATCC 19434 Streptococcus dysgalactiae ATCC 43078 Eubacterium lentum ATCC 43055 Streptococcus equi subsp. equi ATCC 9528 Eubacterium nodutum ATCC 33099 Streptococcus ferus ATCC 33477 Gardnerella vaginalis ATCC 14018 Streptococcus gordonii ATCC 10558 Lactobacillus acidophilus ATCC 4356 Streptococcus macacae ATCC 35911 Lactobacillus crispatus ATCC 33820 Streptococcus mitis ATCC 49456 Lactobacillus gasseri ATCC 33323 Streptococcus mutans ATCC 25175 Lactobacillus johnsonii ATCC 33200 Streptococcus oralis ATCC 35037 Lactococcus lactis subsp. lactis ATCC 19435 Streptococcus parasanguinis ATCC 15912 Lactococcus lactis subsp. lactis ATCC 11454 Streptococcus parauberis DSM 6631 Listeria innocua ATCC 33090 Streptococcus pneumoniae ATCC 27336 Micrococcus luteus ATCC 9341 Streptococcus pyogenes ATCC 19615 Escherichia coli ATCC 25922 Streptococcus ratti ATCC 19645 Micrococcus lylae ATCC 27566 Streptococcus salivarius ATCC 7073 Porphyromonas asaccharolytica ATCC 25260 Streptococcus sanguinis ATCC 10556 Prevotella corporis ATCC 33547 Streptococcus sobrinus ATCC 27352 Prevotella melanogenica ATCC 25845 Streptococcus suis ATCC 43765 Staphylococcus aureus ATCC 13301 Streptococcus uberis ATCC 19436 Staphylococcus epidermidis ATCC 14990 Streptococcus vestubularis ATCC 49124 Staphylococcus saprophyticus ATCC 15305

TABLE 9 Bacterial species used to test the specificity of the Streptococcus agalactiae-specific amplification primers derived from atpD sequences. Strain Reference number Streptococcus acidominimus ATCC 51726 Streptococcus agalactiae ATCC 12400 Streptococcus agalactiae ATCC 12403 Streptococcus agalactiae ATCC 12973 Streptococcus agalactiae ATCC 13813 Streptococcus agalactiae ATCC 27591 Streptococcus agalactiae CDCs-1073 Streptococcus anginosus ATCC 27335 Streptococcus anginosus ATCC 27823 Streptococcus bovis ATCC 33317 Streptococcus cricetus ATCC 19642 Streptococcus cristatus ATCC 51100 Streptococcus downei ATCC 33748 Streptococcus dysgalactiae ATCC 43078 Streptococcus equi subsp. equi ATCC 9528 Streptococcus ferus ATCC 33477 Streptococcus gordonii ATCC 10558 Streptococcus macacae ATCC 35911 Streptococcus mitis ATCC 49456 Streptococcus mutans ATCC 25175 Streptococcus oralis ATCC 35037 Streptococcus parasanguinis ATCC 15912 Streptococcus parauberis DSM 6631 Streptococcus pneumoniae ATCC 27336 Streptococcus pyogenes ATCC 19615 Streptococcus ratti ATCC 19645 Streptococcus salivarius ATCC 7073 Streptococcus sanguinis ATCC 10556 Streptococcus sobrinus ATCC 27352 Streptococcus suis ATCC 43765 Streptococcus uberis ATCC 19436 Streptococcus vestibularis ATCC 49124

TABLE 10 Bacterial species used to test the specificity of the Enterococcus-specific amplification primers derived from tuf sequences. Strain Reference number Gram-positive species (n = 74) Abiotrophia adiacens ATCC 49176 Abiotrophia defectiva ATCC 49175 Bacillus cereus ATCC 14579 Bacillus subtilis ATCC 27370 Bifidobacterium adolescentis ATCC 27534 Bifidobacterium breve ATCC 15700 Bifidobacterium dentium ATCC 27534 Bifidobacterium longum ATCC 15707 Clostridium perfringens ATCC 3124 Clostridium septicum ATCC 12464 Corynebacterium aquaticus ATCC 14665 Corynebacterium ATCC 10700 pseudodiphtheriticum Enterococcus avium ATCC 14025 Enterococcus casseliflavus ATCC 25788 Enterococcus cecorum ATCC 43199 Enterococcus columbae ATCC 51263 Enterococcus dispar ATCC 51266 Enterococcus durans ATCC 19432 Enterococcus faecalis ATCC 29212 Enterococcus faecium ATCC 19434 Enterococcus flavescens ATCC 49996 Enterococcus gallinarum ATCC 49573 Enterococcus hirae ATCC 8044 Enterococcus malodoratus ATCC 43197 Enterococcus mundtii ATCC 43186 Enterococcus pseudoavium ATCC 49372 Enterococcus raffinosus ATCC 49427 Enterococcus saccharolyticus ATCC 43076 Enterococcus solitarius ATCC 49428 Enterococcus sulfureus ATCC 49903 Eubacterium lentum ATCC 49903 Gemella haemolysans ATCC 10379 Gemella morbillorum ATCC 27842 Lactobacillus acidophilus ATCC 4356 Leuconostoc mesenteroides ATCC 19225 Listeria grayi ATCC 19120 Listeria grayi ATCC 19123 Listeria innocua ATCC 33090 Listeria ivanovii ATCC 19119 Listeria monocytogenes ATCC 15313 Listeria seeligeri ATCC 35967 Micrococcus luteus ATCC 9341 Pediococcus acidilacti ATCC 33314 Pediococcus pentosaceus ATCC 33316 Peptococcus niger ATCC 27731 Peptostreptococcus anaerobius ATCC 27337 Peptostreptococcus indolicus ATCC 29247 Peptostreptococcus micros ATCC 33270 Propionibacterium acnes ATCC 6919 Staphylococcus aureus ATCC 43300 Staphylococcus capitis ATCC 27840 Staphylococcus epidermidis ATCC 14990 Staphylococcus haemolyticus ATCC 29970 Staphylococcus hominis ATCC 27844 Staphylococcus lugdunensis ATCC 43809 Staphylococcus saprophyticus ATCC 15305 Staphylococcus simulans ATCC 27848 Staphylococcus warneri ATCC 27836 Streptococcus agalactiae ATCC 13813 Streptococcus anginosus ATCC 33397 Streptococcus bovis ATCC 33317 Streptococcus constellatus ATCC 27823 Streptococcus cristatus ATCC 51100 Streptococcus intermedius ATCC 27335 Streptococcus mitis ATCC 49456 Streptococcus mitis ATCC 3639 Streptococcus mutans ATCC 27175 Streptococcus parasanguinis ATCC 15912 Streptococcus pneumoniae ATCC 27736 Streptococcus pneumoniae ATCC 6303 Streptococcus pyogenes ATCC 19615 Streptococcus salivarius ATCC 7073 Streptococcus sanguinis ATCC 10556 Streptococcus suis ATCC 43765 Gram-negative species (n = 39) Acidominococcus fermentans ATCC 2508 Acinetobacter baumannii ATCC 19606 Alcaligenes faecalis ATCC 8750 Anaerobiospirillum ATCC 29305 succiniproducens Anaerorhabdus furcosus ATCC 25662 Bacteroides distasonis ATCC 8503 Bacteroides thetaiotaomicron ATCC 29741 Bacteroides vulgatus ATCC 8482 Bordetella pertussis LSPQ 3702 Bulkholderia cepacia LSPQ 2217 Butyvibrio fibrinosolvens ATCC 19171 Cardiobacterium hominis ATCC 15826 Citrobacter freundii ATCC 8090 Desulfovibrio vulgaris ATCC 29579 Edwardsiellae tarda ATCC 15947 Enterobacter cloacae ATCC 13047 Escherichia coli ATCC 25922 Fusobacterium russii ATCC 25533 Haemophilus influenzae ATCC 9007 Hafnia alvei ATCC 13337 Klebsiella oxytoca ATCC 13182 Meganomonas hypermegas ATCC 25560 Mitsukoella multiacidus ATCC 27723 Moraxella catarrhalis ATCC 43628 Morganella morganii ATCC 25830 Neisseria meningitidis ATCC 13077 Pasteurella aerogenes ATCC 27883 Proteus vulgaris ATCC 13315 Providencia alcalifaciens ATCC 9886 Providencia rettgeri ATCC 9250 Pseudomonas aeruginosa ATCC 27853 Salmonella typhimurium ATCC 14028 Serratia marcescens ATCC 13880 Shigella flexneri ATCC 12022 Shigella sonnei ATCC 29930 Succinivibrio dextrinosolvens ATCC 19716 Tissierella praeacuta ATCC 25539 Veillonella parvuala ATCC 10790 Yersinia enterocolitica ATCC 9610

TABLE 11 Microbial species for which tuf and/or atpD and/or recA sequences are available in public databases. Species Strain Accession number Coding gene* tuf sequences Bacteria Actinobacillus actinomycetemcomitans HK1651 Genome project² tuf Actinobacillus actinomycetemcomitans HK1651 Genome project² tuf (EF-G) Agrobacterium tumefaciens X99673 tuf Agrobacterium tumefaciens X99673 tuf (EF-G) Agrobacterium tumefaciens X99674 tuf Anacystis nidulans PCC 6301 X17442 tuf Aquifex aeolicus VF5 AE000669 tuf Aquifex aeolicus VF5 AE000669 tuf (EF-G) Aquifex pyrophilus Genome project² tuf (EF-G) Aquifex pyrophilus Y15787 tuf Bacillus anthracis Ames Genome project² tuf Bacillus anthracis Ames Genome project² tuf (EF-G) Bacillus halodurans C-125 AB017508 tuf Bacillus halodurans C-125 AB017508 tuf (EF-G) Bacillus stearothermophilus CCM 2184 AJ000260 tuf Bacillus subtilis 168 D64127 tuf Bacillus subtilis 168 D64127 tuf (EF-G) Bacillus subtilis DSM 10 Z99104 tuf Bacillus subtilis DSM 10 Z99104 tuf (EF-G) Bacteroides forsythus ATCC 43037 AB035466 tuf Bacteroides fragilis DSM 1151 —¹ tuf Bordetella bronchiseptica RB50 Genome project² tuf Bordetella pertussis Tohama 1 Genome project² tuf Bordetella pertussis Tohama 1 Genome project² tuf (EF-G) Borrelia burdorgferi B31 U78193 tuf Borrelia burgdorferi AE001155 tuf (EF-G) Brevibacterium linens DSM 20425 X76863 tuf Buchnera aphidicola Ap Y12307 tuf Burkholderia pseudomallei K96243 Genome project² tuf (EF-G) Campylobacter jejuni NCTC 11168 Y17167 tuf Campylobacter jejuni NCTC 11168 CJ11168X2 tuf (EF-G) Chlamydia pneumoniae CWL029 AE001592 tuf Chlamydia pneumoniae CWL029 AE001639 tuf (EF-G) Chlamydia trachomatis M74221 tuf Chlamydia trachomatis D/UW-3/CX AE001317 tuf (EF-G) Chlamydia trachomatis D/UW-3/CX AE001305 tuf Chlamydia trachomatis F/IC-Cal-13 L22216 tuf Chlorobium vibrioforme DSM 263 X77033 tuf Chloroflexus aurantiacus DSM 636 X76865 tuf Clostridium acetobutylicum ATCC 824 Genome project² tuf Clostridium difficile 630 Genome project² tuf Clostridium difficile 630 Genome project² tuf (EF-G) Corynebacterium diphtheriae NCTC 13129 Genome project² tuf Corynebacterium diphtheriae NCTC 13129 Genome project² tuf (EF-G) Corynebacterium glutamicum ASO 19 X77034 tuf Corynebacterium glutamicum MJ-233 E09634 tuf Coxiella burnetii Nine Mile phase I AF136604 tuf Cytophaga lytica DSM 2039 X77035 tuf Deinococcus radiodurans R1 AE001891 tuf (EF-G) Deinococcus radiodurans R1 AE180092 tuf Deinococcus radiodurans R1 AE002041 tuf Deinonema sp. —¹ tuf Eikenella corrodens ATCC 23834 Z12610 tuf Eikenella corrodens ATCC 23834 Z12610 tuf (EF-G) Enterococcus faecalis Genome project² tuf (EF-G) Escherichia coli J01690 tuf Escherichia coli J01717 tuf Escherichia coli X00415 tuf (EF-G) Escherichia coli X57091 tuf Escherichia coli K-12 MG1655 U00006 tuf Escherichia coli K-12 MG1655 U00096 tuf Escherichia coli K-12 MG1655 AE000410 tuf (EF-G) Fervidobacterium islandicum DSM 5733 Y15788 tuf Fibrobacter succinogenes S85 X76866 tuf Flavobacterium ferrigeneum DSM 13524 X76867 tuf Flexistipes sinusarabici X59461 tuf Gloeobacter violaceus PCC 7421 U09433 tuf Gloeothece sp. PCC 6501 U09434 tuf Haemophilus actinomycetemcomitans HK1651 Genome project² tuf Haemophilus ducreyi 35000 AF087414 tuf (EF-G) Haemophilus influenzae Rd U32739 tuf Haemophilus influenzae Rd U32746 tuf Haemophilus influenzae Rd U32739 tuf (EF-G) Helicobacter pylori 26695 AE000511 tuf Helicobacter pylori J99 AE001539 tuf (EF-G) Helicobacter pylori J99 AE001541 tuf Herpetosiphon aurantiacus Hpga1 X76868 tuf Klebsiella pneumoniae M6H 78578 Genome project² tuf Klebsiella pneumoniae M6H 78578 Genome project² tuf (EF-G) Lactobacillus paracasei E13922 tuf Legionella pneumophila Philadelphia-1 Genome project² tuf Leptospira interrogans AF115283 tuf Leptospira interrogans AF115283 tuf (EF-G) Micrococcus luteus IFO 3333 M17788 tuf (EF-G) Micrococcus luteus IFO 3333 M17788 tuf Moraxella sp. TAC II 25 AJ249258 tuf Mycobacterium avium 104 Genome project² tuf Mycobacterium avium 104 Genome project² tuf (EF-G) Mycobacterium bovis AF2122/97 Genome project² tuf Mycobacterium bovis AF2122/97 Genome project² tuf (EF-G) Mycobacterium leprae L13276 tuf Mycobacterium leprae Z14314 tuf Mycobacterium leprae Z14314 tuf (EF-G) Mycobacterium leprae Thai 53 D13869 tuf Mycobacterium tuberculosis Erdmann S40925 tuf Mycobacterium tuberculosis H37Rv AL021943 tuf (EF-G) Mycobacterium tuberculosis H37Rv Z84395 tuf Mycobacterium tuberculosis y42 AD000005 tuf Mycobacterium tuberculosis CSU#93 Genome project² tuf Mycobacterium tuberculosis CSU#93 Genome project² tuf (EF-G) Mycoplasma capricolum PG-31 X16462 tuf Mycoplasma genitalium G37 U39732 tuf Mycoplasma genitalium G37 U39689 tuf (EF-G) Mycoplasma hominis X57136 tuf Mycoplasma hominis PG21 M57675 tuf Mycoplasma pneumoniae M129 AE000019 tuf Mycoplasma pneumoniae M129 AE000058 tuf (EF-G) Neisseria gonorrhoeae MS11 L36380 tuf Neisseria gonorrhoeae MS11 L36380 tuf (EF-G) Neisseria meningitidis Z2491 Genome project² tuf (EF-G) Neisseria meningitidis Z2491 Genome project² tuf Pasteurella multocida Pm70 Genome project² tuf Peptococcus niger DSM 20745 X76869 tuf Phormidium ectocarpi PCC 7375 U09443 tuf Planobispora rosea ATCC 53773 U67308 tuf Planobispora rosea ATCC 53733 X98830 tuf Planobispora rosea ATCC 53733 X98830 tuf (EF-G) Plectonema boryanum PCC 73110 U09444 tuf Porphyromonas gingivalis W83 Genome project² tuf Porphyromonas gingivalis W83 Genome project² tuf (EF-G) Porphyromonas gingivalis FDC 381 AB035461 tuf Porphyromonas gingivalis W83 AB035462 tuf Porphyromonas gingivalis SUNY 1021 AB035463 tuf Porphyromonas gingivalis A7A1-28 AB035464 tuf Porphyromonas gingivalis ATCC 33277 AB035465 tuf Porphyromonas gingivalis ATCC 33277 AB035471 tuf (EF-G) Prochlorothrix hollandica U09445 tuf Pseudomonas aeruginosa PAO-1 Genome project² tuf Pseudomonas putida Genome project² tuf Rickettsia prowazekii Madrid E AJ235272 tuf Rickettsia prowazekii Madrid E AJ235270 tuf (EF-G) Rickettsia prowazekii Madrid E Z54171 tuf (EF-G) Salmonella choleraesuis subsp. X64591 tuf (EF-G) choleraesuis serotype Typhimurium Salmonella choleraesuis subsp. LT2 trpE91 X55116 tuf choleraesuis serotype Typhimurium Salmonella choleraesuis subsp. LT2 trpE91 X55117 tuf choleraesuis serotype Typhimurium Serpulina hyodysenteriae B204 U51635 tuf Serratia marcescens AF058451 tuf Shewanella putrefaciens DSM 50426 —¹ tuf Shewanella putrefaciens MR-1 Genome project² tuf Spirochaeta aurantia DSM 1902 X76874 tuf Staphylococcus aureus AJ237696 tuf (EF-G) Staphylococcus aureus EMRSA-16 Genome project² tuf Staphylococcus aureus NCTC 8325 Genome project² tuf Staphylococcus aureus COL Genome project² tuf Staphylococcus aureus EMRSA-16 Genome project² tuf (EF-G) Stigmatella aurantiaca DW4 X82820 tuf Stigmatella aurantiaca Sg a1 X76870 tuf Streptococcus mutans GS-5 Kuramitsu U75481 tuf Streptococcus mutans UAB159 Genome project² tuf Streptococcus oralis NTCC 11427 P331701 tuf Streptococcus pyogenes Genome project² tuf (EF-G) Streptococcus pyogenes M1-GAS Genome project² tuf Streptomyces aureofaciens ATCC 10762 AF007125 tuf Streptomyces cinnamoneus Tue89 X98831 tuf Streptomyces coelicolor A3(2) AL031013 tuf (EF-G) Streptomyces coelicolor A3(2) X77039 tuf (EF-G) Streptomyces coelicolor M145 X77039 tuf Streptomyces collinus BSM 40733 S79408 tuf Streptomyces netropsis Tu1063 AF153618 tuf Streptomyces ramocissimus X67057 tuf Streptomyces ramocissimus X67058 tuf Streptomyces ramocissimus X67057 tuf (EF-G) Synechococcus sp. PCC 6301 X17442 tuf (EF-G) Synechococcus sp. PCC 6301 X17442 tuf Synechocystis sp. PCC 6803 D90913 tuf (EF-G) Synechocystis sp. PCC 6803 D90913 tuf Synechocystis sp. PCC 6803 X65159 tuf (EF-G) Taxeobacter occealus Myx 2105 X77036 tuf Thermotoga maritima Genome project² tuf (EF-G) Thermotoga maritima M27479 tuf Thermus aquaticus EP 00276 X66322 tuf Thermus thermophilus HB8 X16278 tuf (EF-G) Thermus thermophilus HB8 X05977 tuf Thermus thermophilus HB8 X06657 tuf Thiomonas cuprina DSM 5495 U78300 tuf Thiomonas cuprina DSM 5495 U78300 tuf (EF-G) Thiomonas cuprina Hoe5 X76871 tuf Treponema denticola Genome project² tuf Treponema denticola Genome project² tuf (EF-G) Treponema pallidum AE001202 tuf Treponema pallidum AE001222 tuf (EF-G) Treponema pallidum AE001248 tuf (EF-G) Ureaplasma urealyticum ATCC 33697 Z34275 tuf Ureaplasma urealyticum serovar 3 biovar 1 AE002151 tuf Ureaplasma urealyticum serovar 3 biovar 1 AE002151 tuf (EF-G) Vibrio cholerae N16961 Genome project² tuf Wolinella succinogenes DSM 1740 X76872 tuf Yersinia pestis CO-92 Genome project² tuf Yersinia pestis CO-92 Genome project² tuf (EF-G) Archaebacteria Archaeoglobus fulgidus Genome project² tuf (EF-G) Halobacterium marismortui X16677 tuf Methanobacterium thermoautrophicum delta H AE000877 tuf Methanococcus jannaschii ATCC 43067 U67486 tuf Methanococcus vannielii X05698 tuf Pyrococcus abyssi Orsay AJ248285 tuf Thermoplasma acidophilum DSM 1728 X53866 tuf Fungi Absidia glauca CBS 101.48 X54730 tuf (EF-1) Arxula adeninivorans Ls3 Z47379 tuf (EF-1) Aspergillus oryzae KBN616 AB007770 tuf (EF-1) Aureobasidium pullulans R106 U19723 tuf (EF-1) Candida albicans SC5314 Genome project² tuf (M) Candida albicans SC5314 M29934 tuf (EF-1) Candida albicans SC5314 M29935 tuf (EF-1) Cryptococcus neoformans B3501 U81803 tuf (EF-1) Cryptococcus neoformans M1-106 U81804 tuf (EF-1) Eremothecium gossypii ATCC 10895 X73978 tuf (EF-1) Eremothecium gossypii A29820 tuf (EF-1) Fusarium oxysporum NRRL 26037 AF008498 tuf (EF-1) Histoplasma capsulatum 186AS U14100 tuf (EF-1) Podospora anserina X74799 tuf (EF-1) Podospora curvicolla VLV X96614 tuf (EF-1) Prototheca wickerhamii 263-11 AJ245645 tuf (EF-1) Puccinia graminis race 32 X73529 tuf (EF-1) Reclinomonas americana ATCC 50394 AF007261 tuf (M) Rhizomucor racemosus ATCC 1216B X17475 tuf (EF-1) Rhizomucor racemosus ATCC 1216B J02605 tuf (EF-1) Rhizomucor racemosus ATCC 1216B X17476 tuf (EF-1) Rhodotorula mucilaginosa AF016239 tuf (EF-1) Saccharomyces cerevisiae K00428 tuf (M) Saccharomyces cerevisiae M59369 tuf (EF-G) Saccharomyces cerevisiae X00779 tuf (EF-1) Saccharomyces cerevisiae X01638 tuf (EF-1) Saccharomyces cerevisiae M10992 tuf (EF-1) Saccharomyces cerevisiae Alpha S288 X78993 tuf (EF-1) Saccharomyces cerevisiae M15666 tuf (EF-1) Saccharomyces cerevisiae Z35987 tuf (EF-1) Saccharomyces cerevisiae S288C (AB972) U51033 tuf (EF-1) Schizophyllum commune 1-40 X94913 tuf (EF-1) Schizosaccharomyces pombe 972h- AL021816 tuf (EF-1) Schizosaccharomyces pombe 972h- AL021813 tuf (EF-1) Schizosaccharomyces pombe 972h- D82571 tuf (EF-1) Schizosaccharomyces pombe U42189 tuf (EF-1) Schizosaccharomyces pombe PR745 D89112 tuf (EF-1) Sordaria macrospora OOO X96615 tuf (EF-1) Trichoderma reesei QM9414 Z23012 tuf (EF-1) Yarrowia lipolytica AF054510 tuf (EF-1) Parasites Blastocystis hominis HE87-1 D64080 tuf (EF-1) Cryptosporidium parvum U69697 tuf (EF-1) Eimeria tenella LS18 AI755521 tuf (EF-1) Entamoeba histolytica HM1:IMSS X83565 tuf (EF-1) Entamoeba histolytica NIH 200 M92073 tuf (EF-1) Giardia lamblia D14342 tuf (EF-1) Kentrophoros sp. AF056101 tuf (EF-1) Leishmania amazonensis IFLA/BR/67/PH8 M92653 tuf (EF-1) Leishmania braziliensis U72244 tuf (EF-1) Onchocerca volvulus M64333 tuf (EF-1) Porphyra purpurea Avonport U08844 tuf (EF-1) Plasmodium berghei ANKA AJ224150 tuf (EF-1) Plasmodium falciparum K1 X60488 tuf (EF-1) Plasmodium knowlesi line H AJ224153 tuf (EF-1) Toxoplasma gondii RH Y11431 tuf (EF-1) Trichomonas tenax ATCC 30207 D78479 tuf (EF-1) Trypanosoma brucei LVH/75/ U10562 tuf (EF-1) Trypanosoma cruzi USAMRU-K/18Y L76077 tuf (EF-1) Human and plants Arabidopsis thaliana Columbia X89227 tuf (EF-1) Glycine max Ceresia X89058 tuf (EF-1) Glycine max Ceresia Y15107 tuf (EF-1) Glycine max Ceresia Y15108 tuf (EF-1) Glycine max Maple Arrow X66062 tuf (EF-1) Homo sapiens X03558 tuf (EF-1) Pyramimonas disomata AB008010 tuf atpD sequences Bacteria Acetobacterium woodi DSM 1030 U10505 atpD Actinobacillus actinomycetemcomitans HK1651 Genome project² atpD Bacillus anthracis Ames Genome project² atpD Bacillus firmus OF4 M60117 atpD Bacillus megaterium QM B1551 M20255 atpD Bacillus stearothermophilus D38058 atpD Bacillus stearothermophilus IFO1035 D38060 atpD Bacillus subtilis 168 Z28592 atpD Bacteroides fragilis DSM 2151 M22247 atpD Bordetella bronchiseptica RB50 Genome project² atpD Bordetella pertussis Tohama 1 Genome project² atpD Borrelia burgdorferi B31 AE001122 atpD (V) Burkholderia cepacia DSM50181 X76877 atpD Burkholderia pseudomallei K96243 Genome project² atpD Campylobacter jejuni NCTC 11168 CJ11168X1 atpD Chlamydia pneumoniae Genome project² atpD (V) Chlamydia trachomatis MoPn Genome project² atpD (V) Chlorobium vibrioforme DSM 263 X76873 atpD Citrobacter freundii JEO503 AF037156 atpD Clostridium acetobutylicum ATCC 824 Genome project² atpD Clostridium acetobutylicum DSM 792 AF101055 atpD Clostridium difficile 630 Genome project² atpD Corynebacterium diphtheriae NCTC13129 Genome project² atpD Corynebacterium glutamicum ASO 19 X76875 atpD Corynebacterium glutamicum MJ-233 E09634 atpD Cytophaga lytica DSM 2039 M22535 atpD Enterobacter aerogenes DSM 30053 —³ atpD Enterococcus faecalis V583 Genome project² atpD (V) Enterococcus hirae M90060 atpD Enterococcus hirae ATCC 9790 D17462 atpD (V) Escherichia coli J01594 atpD Escherichia coli M25464 atpD Escherichia coli V00267 atpD Escherichia coli V00311 atpD Escherichia coli K12 MG1655 L10328 atpD Flavobacterium ferrugineum DSM 13524 —³ atpD Haemophilus actinomycetemcomitans Genome project² atpD Haemophilus influenzae Rd U32730 atpD Helicobacter pylori NCTC 11638 AF004014 atpD Helicobacter pylori 26695 Genome project² atpD Helicobacter pylori J99 Genome project² atpD Klebsiella pneumoniae M6H 78578 Genome project² atpD Lactobacillus casei DSM 20021 X64542 atpD Legionella pneumophila Philadelphia-1 Genome project² atpD Moorella thermoacetica ATCC 39073 U64318 atpD Mycobacterium avium 104 Genome project² atpD Mycobacterium bovis AF2122/97 Genome project² atpD Mycobacterium leprae U15186 atpD Mycobacterium leprae Genome project² atpD Mycobacterium tuberculosis H37Rv Z73419 atpD Mycobacterium tuberculosis CSU#93 Genome project² atpD Mycoplasma gallisepticum X64256 atpD Mycoplasma genitalium G37 U39725 atpD Mycoplasma pneumoniae M129 U43738 atpD Neisseria gonorrhoeae FA 1090 Genome project² atpD Neisseria meningitidis Z2491 Genome project² atpD Pasteurella multocida Pm70 Genome project² atpD Pectinatus frisingensis DSM 20465 X64543 atpD Peptococcus niger DSM 20475 X76878 atpD Pirellula marina IFAM 1313 X57204 atpD Porphyromonas gingivalis W83 Genome project² atpD (V) Propionigenium modestum DSM 2376 X58461 atpD Pseudomonas aeruginosa PAO1 Genome project² atpD Pseudomonas putida Genome project² atpD Rhodobacter capsulatus B100 X99599 atpD Rhodospirillum rubrum X02499 atpD Rickettsia prowazekii F-12 AF036246 atpD Rickettsia prowazekii Madrid Genome project² atpD Ruminococcus albus 7ATCC AB006151 atpD Salmonella bongori JEO4162 AF037155 atpD Salmonella bongori BR1859 AF037154 atpD Salmonella choleraesuis S83769 AF037146 atpD subsp. arizonae Salmonella choleraesuis u24 AF037147 atpD subsp. arizonae Salmonella choleraesuis subsp. K228 AF037140 atpD choleraesuis serotype Dublin Salmonella choleraesuis subsp. K771 AF037139 atpD choleraesuis serotype Dublin Salmonella choleraesuis subsp. Div36-86 AF037142 atpD choleraesuis serotype Infantis Salmonella choleraesuis subsp. Div95-86 AF037143 atpD choleraesuis serotype Tennessee Salmonella choleraesuis subsp. LT2 AF037141 atpD choleraesuis serotype Typhimurium Salmonella choleraesuis DS210/89 AF037149 atpD subsp. diarizonae Salmonella choleraesuis JEO307 AF037148 atpD subsp. diarizonae Salmonella choleraesuis S109671 AF037150 atpD subsp. diarizonae Salmonella choleraesuis S84366 AF037151 atpD subsp. houtenae Salmonella choleraesuis S84098 AF037152 atpD subsp. houtenae Salmonella choleraesuis BR2047 AF037153 atpD subsp. indica Salmonella choleraesuis NSC72 AF037144 atpD subsp. salamae Salmonella choleraesuis S114655 AF037145 atpD subsp. salamae Shewanella putrefaciens MR-1 Genome project² atpD Staphylococcus aureus COL Genome project² atpD Stigmatella aurantiaca Sga1 X76879 atpD Streptococcus bovis JB-1 AB009314 atpD Streptococcus mutans GS-5 U31170 atpD Streptococcus mutans UAB159 Genome project² atpD Streptococcus pneumoniae Type 4 Genome project² atpD (V) Streptococcus pneumoniae Type 4 Genome project² atpD Streptococcus pyogenes M1-GAS Genome project² atpD (V) Streptococcus pyogenes M1-GAS Genome project² atpD Streptococcus sanguinis 10904 AF001955 atpD Streptomyces lividans 1326 Z22606 atpD Thermus thermophilus HB8 D63799 atpD (V) Thiobacillus ferrooxidans ATCC 33020 M81087 atpD Treponema pallidum Nichols AE001228 atpD (V) Vibrio alginolyticus X16050 atpD Vibrio cholerae N16961 Genome project² atpD Wolinella succinogenes DSM 1470 X76880 atpD Yersinia enterocolitica NCTC 10460 AF037157 atpD Yersinia pestis CO-92 Genome project² atpD Archaebacteria Archaeoglobus fulgidus DSM 4304 AE001023 atpD (V) Halobacterium salinarum S56356 atpD (V) Haloferax volcanii WR 340 X79516 atpD Methanococcus jannaschii DSM 2661 U67477 atpD (V) Methanosarcina barkeri DSM 800 J04836 atpD (V) Fungi Candida albicans SC5314 Genome project² atpD Candida tropicalis M64984 atpD (V) Kluyveromyces lactis 2359/152 U37764 atpD Neurospora crassa X53720 atpD Saccharomyces cerevisiae M12082 atpD Saccharomyces cerevisiae X2180-1A J05409 atpD (V) Schizosaccharomyces pombe 972 h- S47814 atpD (V) Schizosaccharomyces pombe 972 h- M57956 atpD Parasites Giardia lamblia WB U18938 atpD Plasmodium falciparum 3D7 L08200 atpD (V) Trypanosoma congolense IL3000 Z25814 atpD (V) Human and plants Homo sapiens L09234 atpD (V) Homo sapiens M27132 atpD recA sequences Bacteria Acetobacter aceti no. 1023 S60630 recA Acetobacter altoacetigenes MH-24 E05290 recA Acetobacter polyoxogenes NBI 1028 D13183 recA Acholeplasma laidlawii 8195 M81465 recA Acidiphilium facilis ATCC 35904 D16538 recA Acidothermus cellulolyticus ATCC 43068 AJ006705 recA Acinetobacter calcoaceticus BD413/ADP1 L26100 recA Actinobacillus actinomycetemcomitans HK1651 Genome project² recA Aeromonas salmonicida A449 U83688 recA Agrobacterium tumefaciens C58 L07902 recA Allochromatium vinosum AJ000677 recA Aquifex aeolicus VF5 AE000775 recA Aquifex pyrophilus Kol5a L23135 recA Azotobacter vinelandii S96898 recA Bacillus stearothermophilus 10 Genome project² recA Bacillus subtilis PB1831 U87792 recA Bacillus subtilis 168 Z99112 recA Bacteroides fragilis M63029 recA Bifidobacterium breve NCFB 2258 AF094756 recA Blastochloris viridis DSM 133 AF022175 recA Bordetella pertussis 165 X53457 recA Bordetella pertussis Tohama I Genome project² recA Borrelia burgdorferi Sh-2-82 U23457 recA Borrelia burgdorferi B31 AE001124 recA Brevibacterium flavum MJ-233 E10390 recA Brucella abortus 2308 L00679 recA Burkholderia cepacia ATCC 17616 U70431 recA Burkholderia cepacia D90120 recA Burkholderia pseudomallei K96243 Genome project² recA Campylobacter fetus subsp. fetus 23D AF020677 recA Campylobacter jejuni 81-176 U03121 recA Campylobacter jejuni NCTC 11168 AL139079 recA Chlamydia trachomatis L2 U16739 recA Chlamydia trachomatis D/UW-3/CX AE001335 recA Chlamydophila pneumoniae CWL029 AE001658 recA Chloroflexus aurantiacus J-10-fl AF037259 recA Clostridium acetobutylicum M94057 recA Clostridium perfringens 13 U61497 recA Corynebacterium diphtheriae NCTC13129 Genome project² recA Corynebacterium glutamicum AS019 U14965 recA Corynebacterium pseudotuberculosis C231 U30387 recA Deinococcus radiodurans KD8301 AB005471 recA Deinococcus radiodurans R1 U01876 recA Enterobacter agglomerans 339 L03291 recA Enterococcus faecalis OGIX M81466 recA Erwinia carotovora X55554 recA Escherichia coli J01672 recA Escherichia coli X55552 recA Escherichia coli K-12 AE000354 recA Frankia alni Arl3 AJ006707 recA Gluconobacter oxydans U21001 recA Haemophilus influenzae Rd U32687 recA Haemophilus influenzae Rd U32741 recA Haemophilus influenzae Rd L07529 recA Helicobacter pylori 69A Z35478 recA Helicobacter pylori 26695 AE000536 recA Helicobacter pylori J99 AE001453 recA Klebsiella pneumoniae M6H 78578 Genome project² recA Lactococcus lactis ML3 M88106 recA Legionella pneumophila X55453 recA Leptospira biflexa serovar patoc U32625 recA Leptospira interrogans serovar pomona U29169 recA Magnetospirillum magnetotacticum MS-1 X17371 recA Methylobacillus flagellatus MFK1 M35325 recA Methylomonas clara ATCC 31226 X59514 recA Mycobacterium avium 104 Genome project² recA Mycobacterium bovis AF122/97 Genome project² recA Mycobacterium leprae X73822 recA Mycobacterium tuberculosis H37Rv X58485 recA Mycobacterium tuberculosis CSU#93 Genome project² recA Mycoplasma genitalium G37 U39717 recA Mycoplasma mycoides GM9 L22073 recA Mycoplasma pneumoniae ATCC 29342 MPAE000033 recA Mycoplasma pulmonis KD735 L22074 recA Myxococcus xanthus L40368 recA Myxococcus xanthus L40367 recA Neisseria animalis NCTC 10212 U57910 recA Neisseria cinerea LCDC 81-176 AJ223869 recA Neisseria cinerea LNP 1646 U57906 recA Neisseria cinerea NCTC 10294 AJ223871 recA Neisseria cinerea Vedros M601 AJ223870 recA Neisseria elongata CCUG 2131 AJ223882 recA Neisseria elongata CCUG 4165A AJ223880 recA Neisseria elongata NCTC 10660 AJ223881 recA Neisseria elongata NCTC 11050 AJ223878 recA Neisseria elongata NHITCC 2376 AJ223877 recA Neisseria elongata CCUG 4557 AJ223879 recA subsp. intermedia Neisseria flava Bangor 9 AJ223873 recA Neisseria flavescens LNP 444 U57907 recA Neisseria gonorrhoeae CH95 U57902 recA Neisseria gonorrhoeae FA19 X64842 recA Neisseria gonorrhoeae MS11 X17374 recA Neisseria gonorrhoeae Genome project² recA Neisseria lactamica CCUC 7757 AJ223866 recA Neisseria lactamica CCUG 7852 Y11819 recA Neisseria lactamica LCDC 77-143 Y11818 recA Neisseria lactamica LCDC 80-111 AJ223864 recA Neisseria lactamica LCDC 845 AJ223865 recA Neisseria lactamica NCTC 10617 U57905 recA Neisseria lactamica NCTC 10618 AJ223863 recA Neisseria meningitidis 44/46 X64849 recA Neisseria meningitidis Bangor 13 AJ223868 recA Neisseria meningitidis HF116 X64848 recA Neisseria meningitidis HF130 X64844 recA Neisseria meningitidis HF46 X64847 recA Neisseria meningitidis M470 X64850 recA Neisseria meningitidis N94II X64846 recA Neisseria meningitidis NCTC 8249 AJ223867 recA Neisseria meningitidis P63 X64845 recA Neisseria meningitidis S3446 U57903 recA Neisseria meningitidis FAM18 Genome project² recA Neisseria mucosa LNP 405 U57908 recA Neisseria mucosa Vedros M1801 AJ223875 recA Neisseria perflava CCUG 17915 AJ223876 recA Neisseria perflava LCDC 85402 AJ223862 recA Neisseria pharyngis var. flava NCTC 4590 U57909 recA Neisseria polysaccharea CCUG 18031 Y11815 recA Neisseria polysaccharea CCUG 24845 Y11816 recA Neisseria polysaccharea CCUG 24846 Y11814 recA Neisseria polysaccharea INS MA 3008 Y11817 recA Neisseria polysaccharea NCTC 11858 U57904 recA Neisseria sicca NRL 30016 AJ223872 recA Neisseria subflava NRL 30017 AJ223874 recA Paracoccus denitrificans DSM 413 U59631 recA Pasteurella multocida X99324 recA Porphyromonas gingivalis W83 U70054 recA Prevotella ruminicola JCM 8958 U61227 recA Proteus mirabilis pG1300 X14870 recA Proteus vulgaris X55555 recA Pseudomonas aeruginosa X05691 recA Pseudomonas aeruginosa PAM 7 X52261 recA Pseudomonas aeruginosa PAO12 D13090 recA Pseudomonas fluorescens OE 28.3 M96558 recA Pseudomonas putida L12684 recA Pseudomonas putida PpS145 U70864 recA Rhizobium leguminosarum VF39 X59956 recA biovar viciae Rhizobium phaseoli CNPAF512 X62479 recA Rhodobacter capsulatus J50 X82183 recA Rhodobacter sphaeroides 2.4.1 X72705 recA Rhodopseudomonas palustris N 7 D84467 recA Rickettsia prowazekii Madrid E AJ235273 recA Rickettsia prowazekii Madrid E U01959 recA Serratia marcescens M22935 recA Shigella flexneri X55553 recA Shigella sonnei KNIH104S AF101227 recA Sinorhizobium meliloti 2011 X59957 recA Staphylococcus aureus L25893 recA Streptococcus gordonii Challis V288 L20574 recA Streptococcus mutans UA96 M81468 recA Streptococcus mutans GS-5 M61897 recA Streptococcus pneumoniae Z17307 recA Streptococcus pneumoniae R800 Z34303 recA Streptococcus pyogenes NZ131 U21934 recA Streptococcus pyogenes D471 M81469 recA Streptococcus salivarius M94062 recA subsp. thermophilus Streptomyces ambofaciens DSM 40697 Z30324 recA Streptomyces coelicolor A3(2) AL020958 recA Streptomyces lividans TK24 X76076 recA Streptomyces rimosus R6 X94233 recA Streptomyces venezuelae ATCC10712 U04837 recA Synechococcus sp. PR6 M29495 recA Synechocystis sp. PCC6803 D90917 recA Thermotoga maritima L23425 recA Thermotoga maritima AE001823 recA Thermus aquaticus L20095 recA Thermus thermophilus HB8 D17392 recA Thiobacillus ferrooxidans M26933 recA Treponema denticola Genome project² recA Treponema pallidum Nichols AE001243 recA Vibrio anguillarum M80525 recA Vibrio cholerae 017 X71969 recA Vibrio cholerae 2740-80 U10162 recA Vibrio cholerae 569B L42384 recA Vibrio cholerae M549 AF117881 recA Vibrio cholerae M553 AF117882 recA Vibrio cholerae M645 AF117883 recA Vibrio cholerae M793 AF117878 recA Vibrio cholerae M794 AF117880 recA Vibrio cholerae M967 AF117879 recA Xanthomonas citri XW47 AF006590 recA Xanthomonas oryzae AF013600 recA Xenorhabdus bovienii T228/1 U87924 recA Xenorhabdus nematophilus AN6 AF127333 recA Yersinia pestis 231 X75336 recA Yersinia pestis CO-92 Genome project² recA Fungi, parasites, human and plants Anabaena variabilis ATCC 29413 M29680 recA Arabidopsis thaliana U43652 recA (Rad51) Candida albicans U39808 recA (Dmc1) Coprinus cinereus Okayama-7 U21905 recA (Rad51) Emericella nidulans Z80341 recA (Rad51) Gallus gallus L09655 recA (Rad51) Homo sapiens D13804 recA (Rad51) Homo sapiens D63882 recA (Dmc1) Leishmania major Friedlin AF062379 recA (Rad51) Leishmania major Friedlin AF062380 recA (Dmc1) Mus musculus D58419 recA (Dmc1) Neurospora crassa 74-OR23-1A D29638 recA (Rad51) Saccharomyces cerevisiae D10023 recA (Rad51) Schizosaccharomyces pombe Z22691 recA (Rad51) Schizosaccharomyces pombe 972h- AL021817 recA (Dmc1) Tetrahymena thermophila PB9R AF064516 recA (Rad51) Trypanosoma brucei stock 427 Y13144 recA (Rad51) Ustilago maydis U62484 recA (Rad51) Xenopus laevis D38488 recA (Rad51) Xenopus laevis D38489 recA (Rad51) *tuf indicates tuf sequences, including tuf genes, fusA genes and fusA-tuf intergenic spacers. tuf (C) indicates tuf sequences divergent from main (usually A and B) copies of the elongation factor-Tu tuf (EF-1) indicates tuf sequences of the eukaryotic type (elongation factor 1α) tuf (M) indicates tuf sequences from organellar (mostly mitochondrial) origin atpD indicates atpD sequences of the F-type atpD (V) indicates atpD sequences of the V-Type recA indicates recA sequences recA (Rad51) indicates rad51 sequences or homologs recA (Dmc1) indicates dmc1 sequences or homologs ¹Nucleotides sequences published in Arch. Microbiol. 1990 153: 241-247 ²These sequences are from theTIGR database (http://www.tigr.org/tdb/tdb.html) ³Nucleotides sequences published in FEMS Microbiology Letters 1988 50: 101-106

TABLE 12 Bacterial species used to test the specificity of the Staphylococcus-specific amplification primers derived from tuf sequences. Strain Reference number Staphylococcal species (n = 27) Staphylococcus arlettae ATCC 43957 Staphylococcus aureus ATCC 35844 subsp. anaerobius Staphylococcus aureus ATCC 43300 subsp. aureus Staphylococcus auricularis ATCC 33753 Staphylococcus capitis ATCC 27840 subsp. capitis Staphylococcus caprae ATCC 35538 Staphylococcus carnosus ATCC 51365 Staphylococcus chromogenes ATCC 43764 Staphylococcus cohnii DSM 20260 subsp. urealyticum Staphylococcus delphini ATCC 49171 Staphylococcus epidermidis ATCC 14990 Staphylococcus equorum ATCC 43958 Staphylococcus felis ATCC 49168 Staphylococcus gallinarum ATCC 35539 Staphylococcus haemolyticus ATCC 29970 Staphylococcus hominis ATCC 27844 Staphylococcus hyicus ATCC 11249 Staphylococcus intermedius ATCC 29663 Staphylococcus kloosis ATCC 43959 Staphylococcus lentus ATCC 29070 Staphylococcus lugdunensis ATCC 43809 Staphylococcus saprophyticus ATCC 15305 Staphylococcus schleiferi ATCC 49545 subsp. coagulans Staphylococcus sciuri ATCC 29060 subsp. sciuri Staphylococcus simulans ATCC 27848 Staphylococcus warneri ATCC 27836 Staphylococcus xylosus ATCC 29971 Gram-negative bacteria (n = 33) Acinetobacter baumannii ATCC 19606 Bacteroides distasonis ATCC 8503 Bacteroides fragilis ATCC 25285 Bulkholderia cepacia ATCC 25416 Bordetella pertussis ATCC 9797 Citrobacter freundii ATCC 8090 Enterobacter aerogenes ATCC 13048 Enterobacter cloacae ATCC 13047 Escherichia coli ATCC 25922 Haemophilus influenzae ATCC 8907 Haemophilus parahaemolyticus ATCC 10014 Haemophilus parainfluenzae ATCC 7901 Hafnia alvei ATCC 13337 Kingella indologenes ATCC 25869 Klebsiella oxytoca ATCC 13182 Klebsiella pneumoniae ATCC 13883 Moraxella catarrhalis ATCC 25240 Morganella morganii ATCC 25830 Neisseria gonorrhoeae ATCC 35201 Neisseria meningitidis ATCC 13077 Proteus mirabilis ATCC 25933 Proteus vulgaris ATCC 13315 Providencia rettgeri ATCC 9250 Providencia stuartii ATCC 29914 Pseudomonas aeruginosa ATCC 27853 Pseudomonas fluorencens ATCC 13525 Salmonella choleraesuis ATCC 7001 Salmonella typhimurium ATCC 14028 Serratia marcescens ATCC 8100 Shigella flexneri ATCC 12022 Shigella sonnei ATCC 29930 Stenotrophomonas maltophilia ATCC 13843 Yersinia enterocolitica ATCC 9610 Other Gram-positive bacteria (n = 20) Bacillus subtilis ATCC 27370 Enterococcus avium ATCC 14025 Enterococcus durans ATCC 19432 Enterococcus faecalis ATCC 19433 Enterococcus faecium ATCC 19434 Enterococcus flavescens ATCC 49996 Enterococcus gallinarum ATCC 49573 Lactobacillus acidophilus ATCC 4356 Lactococcus lactis ATCC 11454 Listeria innocua ATCC 33090 Listeria ivanovii ATCC 19119 Listeria monocytogenes ATCC 15313 Macrococcus caseolyticus ATCC 13548 Streptococcus agalactiae ATCC 13813 Streptococcus anginosus ATCC 33397 Streptococcus bovis ATCC 33317 Streptococcus mutans ATCC 25175 Streptococcus pneumoniae ATCC 6303 Streptococcus pyogenes ATCC 19615 Streptococcus salivarius ATCC 7073

TABLE 13 Bacterial species used to test the specificity of the penicillin-resistant Streptococcus pneumoniae assay. Strain Reference number Gram-positive species (n = 67) Abiotrophia adiacens ATCC 49175 Abiotrophia defectiva ATCC 49176 Actinomyces pyogenes ATCC 19411 Bacillus anthracis ATCC 4229 Bacillus cereus ATCC 14579 Bifidobacterium breve ATCC 15700 Clostridium difficile ATCC 9689 Enterococcus avium ATCC 14025 Enterococcus casseliflavus ATCC 25788 Enterococcus dispar ATCC 51266 Enterococcus durans ATCC 19432 Enterococcus faecalis ATCC 29212 Enterococcus faecium ATCC 19434 Enterococcus flavescens ATCC 49996 Enterococcus gallinarum ATCC 49573 Enterococcus hirae ATCC 8043 Enterococcus mundtii ATCC 43186 Enterococcus raffinosus ATCC 49427 Lactobacillus lactis ATCC 19435 Lactobacillus monocytogenes ATCC 15313 Mobiluncus curtisii ATCC 35242 Peptococcus niger ATCC 27731 Peptostreptococcus acones ATCC 6919 Peptostreptococcus anaerobius ATCC 27337 Peptostreptococcus ATCC 2639 asaccharolyticus Peptostreptococcus lactolyticus ATCC 51172 Peptostreptococcus magnus ATCC 15794 Peptostreptococcus prevotii ATCC 9321 Peptostreptococcus tetradius ATCC 35098 Staphylococcus aureus ATCC 25923 Staphylococcus capitis ATCC 27840 Staphylococcus epidermidis ATCC 14990 Staphylococcus haemolyticus ATCC 29970 Staphylococcus hominis ATCC 27844 Staphylococcus lugdunensis ATCC 43809 Staphylococcus saprophyticus ATCC 15305 Staphylococcus simulans ATCC 27848 Staphylococcus. warneri ATCC 27836 Streptococcus acidominimus ATCC 51726 Streptococcus agalactiae ATCC 12403 Streptococcus anginosus ATCC 33397 Streptococcus bovis ATCC 33317 Streptococcus constellatus ATCC 27823 Streptococcus cricetus ATCC 19624 Streptococcus cristatus ATCC 51100 Streptococcus downei ATCC 33748 Streptococcus dysgalactiae ATCC 43078 Streptococcus equi ATCC 9528 Streptococcus ferus ATCC 33477 Streptococcus gordonii ATCC 10558 Streptococcus intermedius ATCC 27335 Streptococcus mitis ATCC 903 Streptococcus mitis LSPQ 2583 Streptococcus mitis ATCC 49456 Streptococcus mutans ATCC 27175 Streptococcus oralis ATCC 10557 Streptococcus oralis ATCC 9811 Streptococcus oralis ATCC 35037 Streptococcus parasanguinis ATCC 15912 Streptococcus parauberis ATCC 6631 Streptococcus rattus ATCC 15912 Streptococcus salivarius ATCC 7073 Streptococcus sanguinis ATCC 10556 Streptococcus suis ATCC 43765 Streptococcus uberis ATCC 19436 Streptococcus vestibularis ATCC 49124 Gram-negative species (n = 33) Actinetobacter baumannii ATCC 19606 Bordetella pertussis ATCC 9797 Citrobacter diversus ATCC 27028 Citrobacter freundii ATCC 8090 Enterobacter aerogenes ATCC 13048 Enterobacter agglomerans ATCC 27155 Enterobacter cloacae ATCC 13047 Escherichia coli ATCC 25922 Haemophilus ducreyi ATCC 33940 Haemophilus haemolyticus ATCC 33390 Haemophilus influenzae ATCC 9007 Haemophilus parainfluenzae ATCC 7901 Hafnia alvei ATCC 13337 Klebsiella oxytoca ATCC 13182 Klebsiella pneumoniae ATCC 13883 Moraxella atlantae ATCC 29525 Moraxella catarrhalis ATCC 43628 Moraxella morganii ATCC 13077 Neisseria gonorrhoeae ATCC 35201 Neisseria meningitidis ATCC 13077 Proteus mirabilis ATCC 25933 Proteus vulgaris ATCC 13315 Providencia alcalifaciens ATCC 9886 Providencia rettgeri ATCC 9250 Providencia rustigianii ATCC 33673 Providencia stuartii ATCC 33672 Pseudomonas aeruginosa ATCC 35554 Pseudomonas fluorescens ATCC 13525 Pseudomonas stutzeri ATCC 17588 Salmonella typhimurium ATCC 14028 Serratia marcescens ATCC 13880 Shigella flexneri ATCC 12022 Yersina enterocolitica ATCC 9610

TABLE 14 Bacterial species (n = 104) detected by the platelet contaminants assay. Abiotrophia adiacens Abiotrophia defective Acinetobacter baumannii Acinetobacter lwoffi Aerococcus viridans Bacillus anthracis

Brucella abortus Burkholderia cepacia Citrobacter diversus Citrobacter freundii Enterobacter aerogenes Enterobacter agglomerans

Enterococcus avium Enterococcus casseliflavus Enterococcus dispar Enterococcus durans Enterococcus faecalis Enterococcus faecium Enterococcus flavescens Enterococcus gallinarum Enterococcus mundtii Enterococcus raffinosus Enterococcus solitarius

Gemella morbillorum Haemophilus ducreyi Haemophilus haemolyticus Haemophilus influenzae Haemophilus parahaemolyticus Haemophilus parainfluenzae Hafnia alvei Kingella kingae

Legionella pneumophila Megamonas hypermegale Moraxella atlantae Moraxella catarrhalis Morganella morganii Neisseria gonorrheae Neisseria meningitidis Pasteurella aerogenes Pasteurella multocida Peptostreptococcus magnus Proteus mirabilis Providencia alcalifaciens Providencia rettgeri Providencia rustigianii Providencia stuartii

Pseudomonas fluorescens Pseudomonas stutzeri Salmonella bangori

Salmonella enteritidis Salmonella gallinarum Salmonella typhimurium Serratia liquefaciens

Shigella flexneri Shigella sonnei

Staphylococcus capitis

Staphylococcus haemolyticus Staphylococcus hominis Staphylococcus lugdunensis Staphylococcus saprophyticus Staphylococcus simulans Staphylococcus warneri Stenotrophomonas maltophilia Streptococcus acidominimus

Streptococcus anginosus Streptococcus bovis Streptococcus constellatus Streptococcus cricetus Streptococcus cristatus Streptococcus dysgalactiae Streptococcus equi Streptococcus ferus Streptococcus gordonii Streptococcus intermedius Streptococcus macacae Streptococcus mitis

Streptococcus oralis Streptococcus parasanguinis Streptococcus parauberis Streptococcus pneumoniae

Streptococcus ratti

Streptococcus sobrinus Streptococcus uberis Streptococcus vestibularis Vibrio cholerae Yersinia enterocolitica Yersinia pestis

Bold characters indicate the major bacterial contaminants found in platelet concentrates.

TABLE 15 Microorganisms identified by commercial systems¹. Abiotrophia adiacens (Streptococcus adjacens) Abiotrophia defectiva (Streptococcus defectivus) Achromobacter species Acidaminococcus fermentans Acinetobacter alcaligenes Acinetobacter anitratus Acinetobacter baumannii Acinetobacter calcoaceticus Acinetobacter calcoaceticus biovar anitratus Acinetobacter calcoaceticus biovar lwoffi Acinetobacter genomospecies Acinetobacter haemolyticus Acinetobacter johnsonii Acinetobacter junii Acinetobacter lwoffii Acinetobacter radioresistens Acinetobacter species Actinobacillus actinomycetemcomitans Actinobacillus capsulatus Actinobacillus equuli Actinobacillus hominis Actinobacillus lignieresii Actinobacillus pleuropneumoniae Actinobacillus species Actinobacillus suis Actinobacillus ureae Actinomyces bovis Actinomyces israelii Actinomyces meyeri Actinomyces naeslundii Actinomyces neuii subsp. anitratus Actinomyces neuii subsp. neuii Actinomyces odontolyticus Actinomyces pyogenes Actinomyces radingae Actinomyces species Actinomyces turicensis Actinomyces viscosus Aerococcus species Aerococcus viridans Aeromonas caviae Aeromonas hydrophila Aeromonas hydrophila group Aeromonas jandaei Aeromonas salmonicida Aeromonas salmonicida subsp. achromogenes Aeromonas salmonicida subsp. masoucida Aeromonas salmonicida subsp. salmonicida Aeromonas schubertii Aeromonas sobria Aeromonas species Aeromonas trota Aeromonas veronii Aeromonas veronii biovar sobria Aeromonas veronii biovar veronii Agrobacterium radiobacter Agrobacterium species Agrobacterium tumefaciens Alcaligenes denitrificans Alcaligenes faecalis Alcaligenes odorans Alcaligenes odorans (Alcaligenes faecalis) Alcaligenes species Alcaligenes xylosoxidans Alcaligenes xylosoxidans subsp. denitrificans Alcaligenes xylosoxidans subsp. xylosoxidans Alloiococcus otitis Anaerobiospirillum succiniciproducens Anaerovibrio lipolytica Arachnia propionica Arcanobacterium (Actinomyces) bemardiae Arcanobacterium (Actinomyces) pyogenes Arcanobacterium haemolyticum Arcobacter cryaerophilus (Campylobacter cryaerophila) Arthrobacter globiformis Arthrobacter species Arxiozyma telluris (Torulopsis pintolopesii) Atopobium minutum (Lactobacillus minutus) Aureobacterium species Bacillus amyloliquefaciens Bacillus anthracis Bacillus badius Bacillus cereus Bacillus circulans Bacillus coagulans Bacillus firmus Bacillus lentus Bacillus licheniformis Bacillus megaterium Bacillus mycoides Bacillus pantothenticus Bacillus pumilus Bacillus species Bacillus sphaericus Bacillus stearothermophilus Bacillus subtilis Bacillus thuringiensis Bacteroides caccae Bacteroides capillosus Bacteroides distasonis Bacteroides eggerthii Bacteroides fragilis Bacteroides merdae Bacteroides ovatus Bacteroides species Bacteroides splanchnicus Bacteroides stercoris Bacteroides thetaiotaomicron Bacteroides uniformis Bacteroides ureolyticus (B. corrodens) Bacteroides vulgatus Bergeyella (Weeksella) zoohelcum Bifidobacterium adolescentis Bifidobacterium bifidum Bifidobacterium breve Bifidobacterium dentium Bifidobacterium infantis Bifidobacterium species Blastoschizomyces (Dipodascus) capitatus Bordetella avium Bordetella bronchiseptica Bordetella parapertussis Bordetella pertussis Bordetella species Borrelia species Branhamella (Moraxella) catarrhalis Branhamella species Brevibacillus brevis Brevibacillus laterosporus Brevibacterium casei Brevibacterium epidermidis Brevibacterium linens Brevibacterium species Brevundimonas (Pseudomonas) diminuta Brevundimonas (Pseudomonas) vesicularis Brevundimonas species Brochothrix thermosphacta Brucella abortus Brucella canis Brucella melitensis Brucella ovis Brucella species Brucella suis Budvicia aquatica Burkholderia (Pseudomonas) cepacia Burkholderia (Pseudomonas) gladioli Burkholderia (Pseudomonas) mallei Burkholderia (Pseudomonas) pseudomallei Burkholderia species Buttiauxella agrestis Campylobacter coli Campylobacter concisus Campylobacter fetus Campylobacter fetus subsp. fetus Campylobacter fetus subsp. venerealis Campylobacter hyointestinalis Campylobacter jejuni subsp. doylei Campylobacter jejuni subsp. jejuni Campylobacter lari Campylobacter lari subsp. UPTC Campylobacter mucosalis Campylobacter species Campylobacter sputorum Campylobacter sputorum subsp. bubulus Campylobacter sputorum subsp. fecalis Campylobacter sputorum subsp. sputorum Campylobacter upsaliensis Candida (Clavispora) lusitaniae Candida (Pichia) guilliermondii Candida (Torulopsis) glabrata Candida albicans Candida boidinii Candida catenulata Candida ciferrii Candida colliculosa Candida conglobata Candida curvata (Cryptococcus curvatus) Candida dattila Candida dubliniensis Candida famata Candida globosa Candida hellenica Candida holmii Candida humicola Candida inconspicua Candida intermedia Candida kefyr Candida krusei Candida lambica Candida magnoliae Candida maris Candida melibiosica Candida membranaefaciens Candida norvegensis Candida norvegica Candida parapsilosis Candida paratropicalis Candida pelliculosa Candida pseudotropicalis Candida pulcherrima Candida ravautii Candida rugosa Candida sake Candida silvicola Candida species Candida sphaerica Candida stellatoidea Candida tenuis Candida tropicalis Candida utilis Candida valida Candida vini Candida viswanathii Candida zeylanoides Capnocytophaga gingivalis Capnocytophaga ochracea Capnocytophaga species Capnocytophaga sputigena Cardiobacterium hominis Camobacterium divergens Camobacterium piscicola CDC group ED-2 CDC group EF4 (Pasteurella sp.) CDC group EF-4A CDC group EF-4B CDC group EQ-Z CDC group HB-5 CDC group II K-2 CDC group IV C-2 (Bordetella-like) CDC group M5 CDC group M6 Cedecea davisae Cedecea lapagei Cedecea neteri Cedecea species Cellulomonas (Oerskovia) turbata Cellulomonas species Chlamydia species Chromobacterium violaceum Chryseobacterium (Flavobacterium) indologenes Chryseobacterium (Flavobacterium) meningosepticum Chryseobacterium gleum Chryseobacterium species Chryseomonas indologenes Citeromyces matritensis Citrobacter amalonaticus Citrobacter braakii Citrobacter diversus Citrobacter farmeri Citrobacter freundii Citrobacter freundii complex Citrobacter koseri Citrobacter sedlakii Citrobacter species Citrobacter werkmanii Citrobacter youngae Clostridium acetobutylicum Clostridium barati Clostridium beijerinckii Clostridium bifermentans Clostridium botulinum Clostridium botulinum (NP) B&F Clostridium botulinum (NP) E Clostridium botulinum (P) A&H Clostridium botulinum (P) F Clostridium botulinum G1 Clostridium botulinum G2 Clostridium butyricum Clostridium cadaveris Clostridium chauvoei Clostridium clostridiiforme Clostridium difficile Clostridium fallax Clostridium glycolicum Clostridium hastiforme Clostridium histolyticum Clostridium innocuum Clostridium limosum Clostridium novyi Clostridium novyi A Clostridium paraputrificum Clostridium perfringens Clostridium putrificum Clostridium ramosum Clostridium septicum Clostridium sordellii Clostridium species Clostridium sphenoides Clostridium sporogenes Clostridium subterminale Clostridium tertium Clostridium tetani Clostridium tyrobutyricum Comamonas (Pseudomonas) acidovorans Comamonas (Pseudomonas) testosteroni Comamonas species Corynebacterium accolens Corynebacterium afermentans Corynebacterium amycolatum Corynebacterium aquaticum Corynebacterium argentoratense Corynebacterium auris Corynebacterium bovis Corynebacterium coyleae Corynebacterium cystitidis Corynebacterium diphtheriae Corynebacterium diphtheriae biotype belfanti Corynebacterium diphtheriae biotype gravis Corynebacterium diphtheriae biotype intermedius Corynebacterium diphtheriae biotype mitis Corynebacterium flavescens Corynebacterium glucuronolyticum Corynebacterium glucuronolyticum- seminale Corynebacterium group A Corynebacterium group A-4 Corynebacterium group A-5 Corynebacterium group ANF Corynebacterium group B Corynebacterium group B-3 Corynebacterium group F Corynebacterium group F-1 Corynebacterium group F-2 Corynebacterium group G Corynebacterium group G-1 Corynebacterium group G-2 Corynebacterium group I Corynebacterium group I-2 Corynebacterium jeikeium (group JK) Corynebacterium kutscheri (C. murium) Corynebacterium macginleyi Corynebacterium minutissimum Corynebacterium pilosum Corynebacterium propinquum Corynebacterium pseudodiphtheriticum Corynebacterium pseudotuberculosis Corynebacterium pyogenes Corynebacterium renale Corynebacterium renale group Corynebacterium seminale Corynebacterium species Corynebacterium striatum (C. flavidum) Corynebacterium ulcerans Corynebacterium urealyticum (group D2) Corynebacterium xerosis Cryptococcus albidus Cryptococcus ater Cryptococcus cereanus Cryptococcus gastricus Cryptococcus humicolus Cryptococcus lactativorus Cryptococcus laurentii Cryptococcus luteolus Cryptococcus melibiosum Cryptococcus neoformans Cryptococcus species Cryptococcus terreus Cryptococcus uniguttulatus Debaryomyces hansenii Debaryomyces marama Debaryomyces polymorphus Debaryomyces species Dermabacter hominis Dermacoccus (Micrococcus) nishinomiyaensis Dietzia species Edwardsiella hoshinae Edwardsiella ictaluri Edwardsiella species Edwardsiella tarda Eikenella corrodens Empedobacter brevis (Flavobacterium breve) Enterobacter aerogenes Enterobacter agglomerans Enterobacter amnigenus Enterobacter amnigenus asburiae (CDC enteric group 17) Enterobacter amnigenus biogroup 1 Enterobacter amnigenus biogroup 2 Enterobacter asburiae Enterobacter cancerogenus Enterobacter cloacae Enterobacter gergoviae Enterobacter hormaechei Enterobacter intermedius Enterobacter sakazakii Enterobacter species Enterobacter taylorae Enterobacter taylorae (CDC enteric group 19) Enterococcus (Streptococcus) cecorum Enterococcus (Streptococcus) faecalis (Group D) Enterococcus (Streptococcus) faecium(Group D) Enterococcus (Streptococcus) saccharolyticus Enterococcus avium (Group D) Enterococcus casseliflavus (Steptococcus faecium subsp. casseliflavus) Enterococcus durans (Streptococcus faecium subsp. durans) (Group D) Enterococcus gallinarum Enterococcus hirae Enterococcus malodoratus Enterococcus mundtii Enterococcus raffinosus Enterococcus species Erwinia amylovora Erwinia carotovora Erwinia carotovora subsp. atroseptica Erwinia carotovora subsp. betavasculorum Erwinia carotovora subsp. carotovora Erwinia chrysanthemi Erwinia cypripedii Erwinia mallotivora Erwinia nigrifluens Erwinia quercina Erwinia rhapontici Erwinia rubrifaciens Erwinia salicis Erwinia species Erysipelothrix rhusiopathiae Erysipelothrix species Escherichia blattae Escherichia coli Escherichia coli A-D Escherichia coli O157:H7 Escherichia fergusonii Escherichia hermannii Escherichia species Escherichia vulneris Eubacterium aerofaciens Eubacterium alactolyticum Eubacterium lentum Eubacterium limosum Eubacterium species Ewingella americana Filobasidiella neoformans Filobasidium floriforme Filobasidium uniguttulatum Flavimonas oryzihabitans Flavobacterium gleum Flavobacterium indologenes Flavobacterium odoratum Flavobacterium species Francisella novicida Francisella philomiragia Francisella species Francisella tularensis Fusobacterium mortiferum Fusobacterium necrogenes Fusobacterium necrophorum Fusobacterium nucleatum Fusobacterium species Fusobacterium varium Gaffkya species Gardnerella vaginalis Gemella haemolysans Gemella morbillorum Gemella species Geotrichum candidum Geotrichum fermentans Geotrichum penicillarum Geotrichum penicillatum Geotrichum species Gordona species Haemophilus aegyptius Haemophilus aphrophilus Haemophilus ducreyi Haemophilus haemoglobinophilus Haemophilus haemolyticus Haemophilus influenzae Haemophilus influenzae biotype I Haemophilus influenzae biotype II Haemophilus influenzae biotype III Haemophilus influenzae biotype IV Haemophilus influenzae biotype V Haemophilus influenzae biotype VI Haemophilus influenzae biotype VII Haemophilus influenzae biotype VIII Haemophilus paragallinarum Haemophilus parahaemolyticus Haemophilus parainfluenzae Haemophilus parainfluenzae biotype I Haemophilus parainfluenzae biotype II Haemophilus parainfluenzae biotype III Haemophilus parainfluenzae biotype IV Haemophilus parainfluenzae biotype V Haemophilus parainfluenzae biotype VI Haemophilus parainfluenzae biotype VII Haemophilus parainfluenzae biotype VIII Haemophilus paraphrohaemolyticus Haemophilus paraphrophilus Haemophilus segnis Haemophilus somnus Haemophilus species Hafnia alvei Hanseniaspora guilliermondii Hanseniaspora uvarum Hanseniaspora valbyensis Hansenula anomala Hansenula holstii Hansenula polymorpha Helicobacter (Campylobacter) cinaedi Helicobacter (Campylobacter) fennelliae Helicobacter (Campylobacter) pylori Issatchenkia orientalis Kingella denitrificans Kingella indologenes Kingella kingae Kingella species Klebsiella ornithinolytica Klebsiella oxytoca Klebsiella planticola Klebsiella pneumoniae subsp. ozaenae Klebsiella pneumoniae subsp. pneumoniae Klebsiella pneumoniae subsp. rhinoscleromatis Klebsiella species Klebsiella terrigena Kloeckera apiculata Kloeckera apis Kloeckera japonica Kloeckera species Kluyvera ascorbata Kluyvera cryocrescens Kluyvera species Kluyveromyces lactis Kluyveromyces marxianus Kluyveromyces thermotolerans Kocuria (Micrococcus) kristinae Kocuria (Micrococcus) rosea Kocuria(Micrococcus) varians Koserella trabulsii Kytococcus (Micrococcus) sedentarius Lactobacillus (Weissella) viridescens Lactobacillus A Lactobacillus acidophilus Lactobacillus B Lactobacillus brevis Lactobacillus buchneri Lactobacillus casei Lactobacillus casei subsp. casei Lactobacillus casei subsp. lactosus Lactobacillus casei subsp. rhamnosus Lactobacillus catenaformis Lactobacillus cellobiosus Lactobacillus collinoides Lactobacillus coprophilus Lactobacillus crispatus Lactobacillus curvatus Lactobacillus delbrueckii subsp. bulgaricus Lactobacillus delbrueckii subsp. delbrueckii Lactobacillus delbrueckii subsp. lactis Lactobacillus fermentum Lactobacillus fructivorans Lactobacillus helveticus Lactobacillus helveticus subsp. jugurti Lactobacillus jensenii Lactobacillus lindneri Lactobacillus minutus Lactobacillus paracasei subsp. paracasei Lactobacillus pentosus Lactobacillus plantarum Lactobacillus salivarius Lactobacillus salivarius var. salicinius Lactobacillus species Lactococcus diacitilactis Lactococcus garvieae Lactococcus lactis subsp. cremoris Lactococcus lactis subsp. diacitilactis Lactococcus lactis subsp. hordniae Lactococcus lactis subsp. lactis Lactococcus plantarum Lactococcus raffinolactis Leclercia adecarboxylata Legionella species Leminorella species Leptospira species Leptotrichia buccalis Leuconostoc (Weissella) paramesenteroides Leuconostoc carnosum Leuconostoc citreum Leuconostoc gelidum Leuconostoc lactis Leuconostoc mesenteroides Leuconostoc mesenteroides subsp. cremoris Leuconostoc mesenteroides subsp. dextranicum Leuconostoc mesenteroides subsp. mesenteroides Leuconostoc species Listeria grayi Listeria innocua Listeria ivanovii Listeria monocytogenes Listeria murrayi Listeria seeligeri Listeria species Listeria welshimeri Megasphaera elsdenii Methylobacterium mesophilicum Metschnikowia pulcherrima Microbacterium species Micrococcus luteus Micrococcus lylae Micrococcus species Mobiluncus curtisii Mobiluncus mulieris Mobiluncus species Moellerella wisconsensis Moraxella (Branhamella) catarrhalis Moraxella atlantae Moraxella bovis Moraxella lacunata Moraxella nonliquefaciens Moraxella osloensis Moraxella phenylpyruvica Moraxella species Morganella morganii Morganella morganii subsp. morganii Morganella morganii subsp. sibonii Mycobacterium africanum Mycobacterium asiaticum Mycobacterium avium Mycobacterium bovis Mycobacterium chelonae Mycobacterium fortuitum Mycobacterium gordonae Mycobacterium kansasii Mycobacterium malmoense Mycobacterium marinum Mycobacterium phlei Mycobacterium scrofulaceum Mycobacterium smegmatis Mycobacterium species Mycobacterium tuberculosis Mycobacterium ulcerans Mycobacterium xenopi Mycoplasma fermentans Mycoplasma hominis Mycoplasma orale Mycoplasma pneumoniae Mycoplasma species Myroides species Neisseria cinerea Neisseria elongata subsp. elongata Neisseria flava Neisseria flavescens Neisseria gonorrhoeae Neisseria lactamica Neisseria meningitidis Neisseria mucosa Neisseria perflava Neisseria polysaccharea Neisseria saprophytes Neisseria sicca Neisseria subflava Neisseria weaveri Neisseria weaveri (CDC group M5) Nocardia species Ochrobactrum anthropi Oerskovia species Oerskovia xanthineolytica Oligella (Moraxella) urethralis Oligella species Oligella ureolytica Paenibacillus alvei Paenibacillus macerans Paenibacillus polymyxa Pantoea agglomerans Pantoea ananas (Erwinia uredovora) Pantoea dispersa Pantoea species Pantoea stewartii Pasteurella (Haemophilus) avium Pasteurella aerogenes Pasteurella gallinarum Pasteurella haemolytica Pasteurella haemolyticus Pasteurella multocida Pasteurella multocida SF Pasteurella multocida subsp. multocida Pasteurella multocida subsp. septica Pasteurella pneumotropica Pasteurella species Pasteurella ureae Pediococcus acidilactici Pediococcus damnosus Pediococcus pentosaceus Pediococcus species Peptococcus niger Peptococcus species Peptostreptococcus anaerobius Peptostreptococcus asaccharolyticus Peptostreptococcus indolicus Peptostreptococcus magnus Peptostreptococcus micros Peptostreptococcus parvulus Peptostreptococcus prevotii Peptostreptococcus productus Peptostreptococcus species Peptostreptococcus tetradius Phaecoccomyces exophialiae Photobacterium damselae Pichia (Hansenula) anomala Pichia (Hansenula) jadinii Pichia (Hansenula) petersonii Pichia angusta (Hansenula polymorpha) Pichia carsonii (P. vini) Pichia etchellsii Pichia farinosa Pichia fermentans Pichia membranaefaciens Pichia norvegensis Pichia ohmeri Pichia spartinae Pichia species Plesiomonas shigelloides Porphyromonas asaccharolytica Porphyromonas endodontalis Porphyromonas gingivalis Porphyromonas levii Prevotella (Bacteroides) buccae Prevotella (Bacteroides) buccalis Prevotella (Bacteroides) corporis Prevotella (Bacteroides) denticola Prevotella (Bacteroides) loescheii Prevotella (Bacteroides) oralis Prevotella (Bacteroides) disiens Prevotella (Bacteroides) oris Prevotella bivia (Bacteroides bivius) Prevotella intermedia (Bacteroides intermedius) Prevotella melaninogenica (Bacteroides melaninogenicus) Prevotella ruminicola Propionibacterium acnes Propionibacterium avidum Propionibacterium granulosum Propionibacterium propionicum Propionibacterium species Proteus mirabilis Proteus penneri Proteus species Proteus vulgaris Prototheca species Prototheca wickerhamii Prototheca zopfii Providencia alcalifaciens Providencia heimbachae Providencia rettgeri Providencia rustigianii Providencia species Providencia stuartii Providencia stuartii urea + Pseudomonas (Chryseomonas) luteola Pseudomonas acidovorans Pseudomonas aeruginosa Pseudomonas alcaligenes Pseudomonas cepacia Pseudomonas chlororaphis (P. aureofaciens) Pseudomonas fluorescens Pseudomonas fluorescens group Pseudomonas mendocina Pseudomonas pseudoalcaligenes Pseudomonas putida Pseudomonas species Pseudomonas stutzeri Pseudomonas testosteroni Pseudomonas vesicularis Pseudoramibacter (Eubacterium) alactolyticus Psychrobacter (Moraxella) phenylpyruvicus Rahnella aquatilis Ralstonia (Pseudomonas, Burkholderia) pickettii Rhodococcus (Corynebacterium) equi Rhodococcus species Rhodosporidium toruloides Rhodotorula glutinis Rhodotorula minuta Rhodotorula mucilaginosa (R. rubra) Rhodotorula species Rickettsia species Rothia dentocariosa Saccharomyces cerevisiae Saccharomyces exiguus Saccharomyces kluyverii Saccharomyces species Sakaguchia dacryoides (Rhodosporidium dacryoidum) Salmonella arizonae Salmonella choleraesuis Salmonella enteritidis Salmonella gallinarum Salmonella paratyphi A Salmonella paratyphi B Salmonella pullorum Salmonella species Salmonella typhi Salmonella typhimurium Salmonella typhisuis Salmonella/Arizona Serratia ficaria Serratia fonticola Serratia grimesii Serratia liquefaciens Serratia marcescens Serratia odorifera Serratia odorifera type 1 Serratia odorifera type 2 Serratia plymuthica Serratia proteamaculans Serratia proteamaculans subsp. proteamaculans Serratia proteamaculans subsp. quinovora Serratia rubidaea Serratia species Shewanella (Pseudomonas, Alteromonas) putrefaciens Shigella boydii Shigella dysenteriae Shigella flexneri Shigella sonneri Shigella species Sphingobacterium multivorum Sphingobacterium species Sphingobacterium spiritivorum Sphingobacterium thalpophilum Sphingomonas (Pseudomonas) paucimobilis Sporidiobolus salmonicolor Sporobolomyces roseus Sporobolomyces salmonicolor Sporobolomyces species Staphylococcus (Peptococcus) saccharolyticus Staphylococcus arlettae Staphylococcus aureus Staphylococcus aureus (Coagulase- negative) Staphylococcus auricularis Staphylococcus capitis Staphylococcus capitis subsp. capitis Staphylococcus capitis subsp. ureolyticus Staphylococcus caprae Staphylococcus carnosus Staphylococcus caseolyticus Staphylococcus chromogenes Staphylococcus cohnii Staphylococcus cohnii subsp. cohnii Staphylococcus cohnii subsp. urealyticum Staphylococcus epidermidis Staphylococcus equorum Staphylococcus gallinarum Staphylococcus haemolyticus Staphylococcus hominis Staphylococcus hominis subsp. hominis Staphylococcus hominis subsp. novobiosepticus Staphylococcus hyicus Staphylococcus intermedius Staphylococcus kloosii Staphylococcus lentus Staphylococcus lugdunensis Staphylococcus saprophyticus Staphylococcus schleiferi Staphylococcus sciuri Staphylococcus simulans Staphylococcus species Staphylococcus warneri Staphylococcus xylosus Stenotrophomonas (Xanthomonas) maltophilia Stephanoascus ciferrii Stomatococcus mucilaginosus Streptococcus acidominimus Streptococcus agalactiae Streptococcus agalactiae (Group B) Streptococcus agalactiae hemolytic Streptococcus agalactiae non- hemolytic Streptococcus alactolyticus Streptococcus anginosus Streptococcus anginosus (Group D, nonenterococci) Streptococcus beta-hemolytic group A Streptococcus beta-hemolytic non- group A or B Streptococcus beta-hemolytic non- group A Streptococcus beta-hemolytic Streptococcus bovis (Group D, nonenterococci) Streptococcus bovis I Streptococcus bovis II Streptococcus canis Streptococcus constellatus Streptococcus constellatus (Streptococcus milleri I) Streptococcus constellatus (viridans Streptococcus) Streptococcus downei Streptococcus dysgalactiae subsp. dysgalactiae Streptococcus dysgalactiae subsp. equisimilis Streptococcus equi (Group C/Group G Streptococcus) Streptococcus equi subsp. equi Streptococcus equi subsp. zooepidemicus Streptococcus equinus Streptococcus equinus (Group D, nonenterococci) Streptococcus equisimilis Streptococcus equisimulis (Group C/Group G Streptococcus) Streptococcus Gamma (non)- hemolytic Streptococcus gordonii Streptococcus Group B Streptococcus Group C Streptococcus Group D Streptococcus Group E Streptococcus Group F Streptococcus Group G Streptococcus Group L Streptococcus Group P Streptococcus Group U Streptococcus intermedius Streptococcus intermedius (Streptococcus milleri II) Streptococcus intermedius (viridans Streptococcus) Streptococcus milleri group Streptococcus mitis Streptococcus mitis (viridans Streptococcus) Streptococcus mitis group Streptococcus mutans Streptococcus mutans (viridans Streptococcus) Streptococcus oralis Streptococcus parasanguis Streptococcus pneumoniae Streptococcus porcinus Streptococcus pyogenes Streptococcus pyogenes (Group A) Streptococcus salivarius Streptococcus salivarius (viridans Streptococcus) Streptococcus salivarius subsp. salivarius Streptococcus salivarius subsp. thermophilus Streptococcus sanguis Streptococcus sanguis I (viridans Streptococcus) Streptococcus sanguis II Streptococcus sanguis II (viridans Streptococcus) Streptococcus sobrinus Streptococcus species Streptococcus suis I Streptococcus suis II Streptococcus uberis Streptococcus uberis (viridans Streptococcus) Streptococcus vestibularis Streptococcus zooepidemicus Streptococcus zooepidemicus (Group C) Streptomyces somaliensis Streptomyces species Suttonella (Kingella) indologenes Tatumella ptyseos Tetragenococcus (Pediococcus) halophilus Torulaspora delbrueckii (Saccharomyces rosei) Torulopsis candida Torulopsis haemulonii Torulopsis inconspicua Treponema species Trichosporon asahii Trichosporon asteroides Trichosporon beigelii Trichosporon cutaneum Trichosporon inkin Trichosporon mucoides Trichosporon ovoides Trichosporon pullulans Trichosporon species Turicella otitidis Ureaplasma species Ureaplasma urealyticum Veillonella parvula (V. alcalescens) Veillonella species Vibrio alginolyticus Vibrio cholerae Vibrio damsela Vibrio fluvialis Vibrio furnissii Vibrio harveyi Vibrio hollisae Vibrio metschnikovii Vibrio mimicus Vibrio parahaemolyticus Vibrio species Vibrio species SF Vibrio vulnificus Weeksella (Bergeylla) virosa Weeksella species Weeksella virosa Williopsis (Hansenula) satumus Xanthomonas campestris Xanthomonas species Yarrowia (Candida) lipolytica Yersinia aldovae Yersinia enterocolitica Yersinia enterocolitica group Yersinia frederiksenii Yersinia intermedia Yersinia intermedius Yersinia kristensenii Yersinia pestis Yersinia pseudotuberculosis Yersinia pseudotuberculosis SF Yersinia ruckeri Yersinia species Yokenella regensburgei Yokenella regensburgei (Koserella trabulsii) Zygoascus hellenicus Zygosaccharomyces species ¹The list includes microorganisms that may be identified by API identification test systems and VITEK ® automated identification system from bioMerieux Inc., or by the MicroScan ®-WalkAway ® automated systems from Dade Behring. Identification relies on classical identification methods using batteries of biochemical and other phenotypical tests.

TABLE 16 tuf gene sequences obtained in our laboratory (Example 42). GenBank Species Strain no. Gene Accession no.* Abiotrophia adiacens ATCC49175 tuf AF124224 Enterococcus avium ATCC14025 tufA AF124220 tufB AF274715 Enterococcus casseliflavus ATCC25788 tufA AF274716 tufB AF274717 Enterococcus cecorum ATCC43198 tuf AF274718 Enterococcus columbae ATCC51263 tuf AF274719 Enterococcus dispar ATCC51266 tufA AF274720 tufB AF274721 Enterococcus durans ATCC19432 tufA AF274722 tufB AF274723 Enterococcus faecalis ATCC29212 tuf AF124221 Enterococcus faecium ATCC 19434 tufA AF124222 tufB AF274724 Enterococcus gallinarum ATCC49573 tufA AF124223 tufB AF274725 Enterococcus hirae ATCC8043 tufA AF274726 tufB AF274727 Enterococcus malodoratus ATCC43197 tufA AF274728 tufB AF274729 Enterococcus mundtii ATCC43186 tufA AF274730 tufB AF274731 Enterococcus pseudoavium ATCC49372 tufA AF274732 tufB AF274733 Enterococcus raffinosus ATCC49427 tufA AF274734 tufB AF274735 Enterococcus saccharolyticus ATCC43076 tuf AF274736 Enterococcus solitarius ATCC49428 tuf AF274737 Enterococcus sulfureus ATCC49903 tuf AF274738 Lactococcus lactis ATCC11154 tuf AF274745 Listeria monocytogenes ATCC15313 tuf AF274746 Listeria seeligeri ATCC35967 tuf AF274747 Staphylococcus aureus ATCC25923 tuf AF274739 Staphylococcus epidermidis ATCC14990 tuf AF274740 Streptococcus mutans ATCC25175 tuf AF274741 Streptococcus pneumoniae ATCC6303 tuf AF274742 Streptococcus pyogenes ATCC19615 tuf AF274743 Streptococcus suis ATCC43765 tuf AF274744 *Corresponding sequence ID NO. for the above ATCC strains are given in table 7.

TABLE 17 tuf gene sequences selected from databases for Example 42. Species Gene Accession no.* Agrobacterium tumefaciens tufA X99673 tufB X99674 Anacystis nidulans tuf X17442 Aquifex aeolicus tufA AE000657 tufB AE000657 Bacillus stearothermophilus tuf AJ000260 Bacillus subtilis tuf AL009126 Bacteroides fragilis tuf P33165 Borrelia burgdorferi tuf AE000783 Brevibacterium linens tuf X76863 Bulkholderia cepacia tuf P33167 Campylobacter jejuni tufB Y17167 Chlamydia pneumoniae tuf AE001363 Chlamydia trachomatis tuf M74221 Corynebacterium glutamicum tuf X77034 Cytophaga lytica tuf X77035 Deinococcus radiodurans tuf AE000513 Escherichia coli tufA J01690 tufB J01717 Fervidobacterium islandicum tuf Y15788 Haemophilus influenzae tufA L42023 tufB L42023 Helicobacter pylori tuf AE000511 Homo sapiens (Human) EF-1α X03558 Methanococcus jannaschii EF-1α U67486 Mycobacterium leprae tuf D13869 Mycobacterium tuberculosis tuf X63539 Mycoplasma genitalium tuf L43967 Mycoplasma pneumoniae tuf U00089 Neisseria gonorrhoeae tufA L36380 Nicotiana tabacum (Tobacco) EF-1α U04632 Peptococcus niger tuf X76869 Planobispora rosea tuf1 U67308 Saccharomyces cerevisiae (Yeast) EF-1α X00779 Salmonella typhimurium tufA X55116 tufB X55117 Shewanella putrefaciens tuf P33169 Spirochaeta aurantia tuf X76874 Spirulina platensis tufA X15646 Streptomyces aureofaciens tuf1 AF007125 Streptomyces cinnamoneus tuf1 X98831 Streptomyces coelicolor tuf1 X77039 tuf3 X77040 Streptomyces collinus tuf1 S79408 Streptomyces ramocissimus tuf1 X67057 tuf2 X67058 tuf3 X67059 Synechocystis sp. tuf AB001339 Taxeobacter ocellatus tuf X77036 Thermotoga maritima tuf AE000512 Thermus aquaticus tuf X66322 Thermus thermophilus tuf X06657 Thiobacillus cuprinus tuf U78300 Treponema pallidum tuf AE000520 Wolinella succinogenes tuf X76872 *Sequence data were obtained from GenBank, EMBL, and SWISSPROT databases. Genes were designated as appeared in the references.

TABLE 18 Nucleotide and amino acid sequence identities of EF-Tu between different enterococci and other low G + C gram-positive bacteria.

The upper right triangle represents the deduced amino acid sequence identities of gram-positive bacterial EF-Tu; while the lower left triangle represents the DNA sequence identities of the corresponding tuf genes. The sequence identities between different enterococcaltufA genes are boxed while those between enterococcaltufB genes are shaded.

TABLE 19 Strains analyzed in Example 43. 16S rDNA sequence accession Taxon Strain* Strain† number Cedecea davisae ATCC 33431^(T) Cedecea lapagei ATCC 33432^(T) Cedecea neteri ATCC 33855^(T) Citrobacter amalonaticus ATCC 25405^(T) CDC 9020-77^(T) AF025370 Citrobacter braakii ATCC 43162 CDC 080-58^(T) AF025368 Citrobacter farmeri ATCC 51112^(T) CDC 2991-81^(T) AF025371 Citrobacter freundii ATCC 8090^(T) DSM 30039^(T) AJ233408 Citrobacter koseri ATCC 27156^(T) Citrobacter sedlakii ATCC 51115^(T) CDC 4696-86^(T) AF025364 Citrobacter werkmanii ATCC 51114^(T) CDC 0876-58^(T) AF025373 Citrobacter youngae ATCC 29935^(T) Edwardsiella hoshinae ATCC 33379^(T) Edwardsiella tarda ATCC 15947^(T) CDC 4411-68 AF015259 Enterobacter aerogenes ATCC 13048^(T) JCM 1235^(T) AB004750 Enterobacter agglomerans ATCC 27989 Enterobacter amnigenus ATCC 33072^(T) JCM 1237^(T) AB004749 Enterobacter asburiae ATCC 35953^(T) JCM 6051^(T) AB004744 Enterobacter cancerogenus ATCC 35317^(T) Enterobacter cloacae ATCC 13047^(T) Enterobacter gergoviae ATCC 33028^(T) JCM 1234^(T) AB004748 Enterobacter hormaechei ATCC 49162^(T) Enterobacter sakazakii ATCC 29544^(T) JCM 1233^(T) AB004746 Escherichia coli ATCC 11775^(T) ATCC 11775^(T) X80725 Escherichia coli ATCC 25922 ATCC 25922 X80724 Escherichia coli (ETEC) ATCC 35401 Escherichia coli (O157:H7) ATCC 43895 ATCC 43895 Z83205 Escherichia fergusonii ATCC 35469^(T) Escherichia hermanii ATCC 33650^(T) Escherichia vulneris ATCC 33821^(T) ATCC 33821^(T) X80734 Ewingella americana ATCC 33852^(T) NCPPB 3905 X88848 Hafnia alvei ATCC 13337^(T) ATCC 13337^(T) M59155 Klebsiella ornithinolytica ATCC 31898 CIP 103.364 U78182 Klebsiella oxytoca ATCC 33496 ATCC 13182^(T) U78183 Klebsiella planticola ATCC 33531^(T) JCM 7251^(T) AB004755 Klebsiella pneumoniae subsp. pneumoniae ATCC 13883^(T) DSM 30104^(T) AJ233420 subsp. ozaenae ATCC 11296^(T) ATCC 11296^(T) Y17654 subsp. rhinoscleromatis ATCC 13884^(T) Kluyvera ascorbata ATCC 33433^(T) ATCC 14236 Y07650 Kluyvera cryocrescens ATCC 33435^(T) Kluyvera georgiana ATCC 51603^(T) Leclercia adecarboxylata ATCC 23216^(T) Leminorella grimontii ATCC 33999^(T) DSM 5078^(T) AJ233421 Moellerella wisconsensis ATCC 35017^(T) Morganella morganii ATCC 25830^(T) Pantoea agglomerans ATCC 27155^(T) DSM 3493^(T) AJ233423 Pantoea dispersa ATCC 14589^(T) Plesiomonas shigelloides ATCC 14029^(T) Pragia fontium ATCC 49100^(T) DSM 5563^(T) AJ233424 Proteus mirabilis ATCC 25933 Proteus penneri ATCC 33519^(T) Proteus vulgaris ATCC 13315^(T) DSM 30118^(T) AJ233425 Providencia alcalifaciens ATCC 9886^(T) Providencia rettgeri ATCC 9250 Providencia rustigianii ATCC 33673^(T) Providencia stuartii ATCC 33672 Rahnella aquatilis ATCC 33071^(T) DSM 4594^(T) AJ233426 Salmonella choleraesuis subsp. arizonae ATCC 13314^(T) subsp. choleraesuis serotype Choleraesuis ATCC 7001 serotype Enteritidis‡ ATCC 13076^(T) SE22 SE22 serotype Gallinarum ATCC 9184 serotype Heidelberg ATCC 8326 serotype Paratyphi A ATCC 9150 serotype Paratyphi B ATCC 8759 serotype Typhi‡ ATCC 10749 St111 U88545 serotype Typhimurium‡ ATCC 14028 serotype Virchow ATCC 51955 subsp. diarizonae ATCC 43973^(T) subsp. houtenae ATCC 43974^(T) subsp. indica ATCC 43976^(T) subsp. salamae ATCC 43972^(T) Serratia fonticola DSM 4576^(T) DSM 4576^(T) AJ233429 Serratia grimesii ATCC 14460^(T) DSM 30063^(T) AJ233430 Serratia liquefaciens ATCC 27592^(T) Serratia marcescens ATCC 13880^(T) DSM 30121^(T) AJ233431 Serratia odorifera ATCC 33077^(T) DSM 4582^(T) AJ233432 Serratia plymuthica DSM 4540^(T) DSM 4540^(T) AJ233433 Serratia rubidaea DSM 4480^(T) DSM 4480^(T) AJ233436 Shigella boydii ATCC 9207 ATCC 9207 X96965 Shigella dysenteriae ATCC 11835 ATCC 13313^(T) X96966 ATCC 25931 X96964 Shigella flexneri ATCC 12022 ATCC 12022 X96963 Shigella sonnei ATCC 29930^(T) Tatumella ptyseos ATCC 33301^(T) DSM 5000^(T) AJ233437 Trabulsiella guamensis ATCC 49490^(T) Yersinia enterocolitica ATCC 9610^(T) ATCC 9610^(T) M59292 Yersinia frederiksenii ATCC 33641^(T) Yersinia intermedia ATCC 29909^(T) Yersinia pestis RRB KIMD27 ATCC 19428^(T) X75274 Yersinia pseudotuberculosis ATCC 29833^(T) Yersinia rohdei ATCC 43380^(T) ER-2935^(T) X75276 Shewanella putrefaciens ATCC 8071^(T) Vibrio cholerae ATCC 25870 ATCC 14035^(T) X74695 T Type strain *Strains used in this study for sequencing of partial tuf and atpD genes. SEQ ID NOs. for tuf and atpD sequences corresponding to the above reference strains are given in table 7. †Strains used in other studies for sequencing of 16S rDNA gene. When both strain numbers are on the same row, both strains are considered to be the same although strain numbers may be different. ‡Phylogenetic serotypes considered species by the Bacteriological Code (1990 Revision).

TABLE 20 PCR primer pairs used in this study Primer Nucleotide Amplicon SEQ ID NO. Sequence positions* length (bp) Tuf 664 5′-AAYATGATIACIGGIGCIGCICARATGGA- 271-299 884 3′ 697 5′-CCIACIGTICKICCRCCYTCRCG-3′ 1132-1156 atpD 568 5′-RTIATIGGIGCIGTIRTIGAYGT-3′ 25-47 884 567 5′-TCRTCIGCIGGIACRTAIAYIGCYTG-3′ 883-908 700 5′-TIRTIGAYGTCGARTTCCCTCARG-3′ 38-61 871 567 5′-TCRTCIGCIGGIACRTAIAYIGCYTG-3′ 883-908 *The nucleotide positions given are for E. coli tuf and atpD sequences (GenBank accession no. AE000410 and V00267, respectively). Numbering starts from the first base of the initiation codon.

TABLE 21 Selection of M. catarrhalis-specific primer pairs from SEQ ID NO: 29¹ (466 pb DNA fragment) other than those previously tested². Amplicon Moraxella Moraxella size catarrhalis catarrhalis Moraxella Primer Sequence (bp) ATCC 43628 ATCC 53879 nonliquefaciens SEQ ID NO: 118 CGCTGACGGCTTGTTTGTACCA 118 +³ + − SEQ ID NO: 119 TGTTTTGAGCTTTTTATTTTTTGA VBmcat1 TGCTTAAGATTCACTCTGCCATTTT 93 + + − VBmcat2 TAAGTCGCTGACGGCTTGTTT VBmcat3 CCTGCACCACAAGTCATCAT 140 + + − VBmcat4 AATTCACCAACAATGTCAAAGC VBmcat5 AATGATAACCAGTCAAGCAAGC 219 + + − VBmcat6 GGTGCATGGTGATTTGTAAAA VBmcat7 GTGTGCGTTCACTTTTACAAAT 160 + + − VBmcat8 GGTGTTAAGCTGATGATGAGAG VBmcat9 TGACCATGCACACCCTTATT 167 + + − VBmcat10 TCATTGGGATGAAAGTATCGTT Moraxella Moraxella Moraxella Moraxella Kingella Kingella Primer lacunata osloensis atlantae phenylpyruvica indologenes kingea SEQ ID NO: 118 − − − − − − SEQ ID NO: 119 VBmcat1 − − − − − − VBmcat2 VBmcat3 − − − − − − VBmcat4 VBmcat5 − − − − − − VBmcat6 VBmcat7 − − − − − − VBmcat8 VBmcat9 − − − − − − VBmcat10 Neisseria Neisseria Escherichia Staphylococcus Primer meningitidis gonorrhoeae coli aureus SEQ ID NO: 118 − − − − SEQ ID NO: 119 VBmcat1 − − − − VBmcat2 VBmcat3 − − − − VBmcat4 VBmcat5 − − − − VBmcat6 VBmcat7 − − − − VBmcat8 VBmcat9 − − − − VBmcat10 ¹SEQ ID NO. from U.S. Pat. No. 6,001,564. ²All PCR assays were performed with 1 ng of purified genomic DNA by using an annealing temperature of 55° C. and 30 cycles of amplification. The genomic DNA from the various bacterial species above was always isolated from reference strains obtained from ATCC. ³All position results showed a strong amplification signal with genomic DNA from the target species M. catarrhalis.

TABLE 22 Selection of S. epidermidis-specific primer pairs from SEQ ID NO: 36¹ (705 pb DNA fragment) other than those previously tested. Amplicon Staphylococcus Staphylococcus Staphylo- Staphylo- size epidermidis, epidermidis, coccus coccus Primer Sequence (all 25 nucleotides) (bp) ATCC 14990 ATCC 12228 capitis cohnii SEQ ID NO: 145 ATCAAAAAGTTGGCGAACCTTTTCA 125 +³ + − − SEQ ID NO: 146 CAAAAGAGCGTGGAGAAAAGTATCA VBsep3 CATAGTCTGATTGCTCAAAGTCTTG 208 + + − − VBsep4 GCGAATAGTGAACTACATTCTGTTG + + − − VBsep5 CACGCTCTTTTGCAATTTCCATTGA 208 + + + + VBsep6 GAAGCAAATATTCAAAATGCACCAG + + + + VBsep7 AAAGTCTTTTGCTTCTTCAGATTCA 177 + + − − VBsep8 GTGTTCACAGGTATGGATGCTCTTA + + NT NT + + NT NT VBsep9 GAGCATCCATACCTGTGAACACAGA 153 + + − − VBsep10 TTTTCCAATTACAAGAGACATCAGT + + NT NT + + NT NT VBsep11 TTTGAATTCGCATGTACTTTGTTTG 135 + + − − VBsep12 CCCCGGGTTCGAAATCGATAAAAAG Staphylo- Staphylo- Staphylo- Staphylo- Staphylo- Entero- coccus coccus Staphylo- coccus Staphylo- Staphylo- coccus coccus Bacillus coccus Primer aureus auricularis coccus hominis coccus coccus simulans warneri subtilis faecalis SEQ ID NO: 145 − − − − − − − − − − SEQ ID NO: 146 VBsep3 − − + − − − − − − − VBsep4 − − − − − − − − − − VBsep5 + − + + − − − − − − VBsep6 + − + + − − − NT NT NT VBsep7 − − + − − − + − − − VBsep8 − NT − NT − − + NT NT NT − NT − NT − − − NT NT NT VBsep9 − − + − + + − − − − VBsep10 − NT + NT + − − NT NT NT − NT − NT − − − NT NT NT VBsep11 − − − − − − − − − − VBsep12 Entero- Entero- Strepto- Strepto- Strepto- Annealing coccus coccus Listeria coccus coccus coccus temperature² Primer faecium gallinarum monocytogenes agalactiae pneumoniae pyogenes (° C.) SEQ ID NO: 145 − − − − − − 55 SEQ ID NO: 146 VBsep3 − − − − − − 55 VBsep4 − − − − − − 60 VBsep5 − − − − − − 55 VBsep6 NT NT NT NT NT NT 65 VBsep7 − − − − − − 55 VBsep8 NT NT NT NT NT NT 60 NT NT NT NT NT NT 65 VBsep9 − − − − − − 55 VBsep10 NT NT NT NT NT NT 60 NT NT NT NT NT NT 65 VBsep11 − − − − − − 55 VBsep12 ¹SEQ ID NO. from U.S. Pat. No. 6,001,564. ²All PCR assays were performed with 1 ng of purified genomic DNA by using an annealing temperature of 55 to 65° C. and 30 cycles of amplification. The genomic DNA from the various bacterial species above was always isolated from reference strains obtained from ATCC. ³All positive results showed a strong amplification signal with genomic DNA from the target species S. epidermidis. The instensity of the positive amplification signal with species other than S. epidermidis was variable. NT = NOT TESTED.

TABLE 23 Influence of nucleotide variation(s) on the efficiency of the PCR amplification: Example with SEQ ID NO: 146 from S. epidermidis. Staphyloccus epidermidis ² Staphylococcus ATCC 14990 aureus ³ Sequence Number of 50° C. 55° C. 50° C. Primer¹ (all 25 nucleotides) mutation 1 1 0.1 0.01 1 SEQ ID NO: 145 ATCAAAAAGTTGGCGAACCTTTTCA 0 SEQ ID NO: 146 CAAAAGAGCGTGGAGAAAAGTATCA 0  3+⁴ 3+ 2+ + − VBmut1 CAAAAGAGCGTGGAGAAAAGTA

CA 1 3+ 3+ 2+ + − VBmut2 CAAAAGAGCGTGGAGAAAA

TATCA 1 3+ 3+ 2+ + − VBmut3 CAAAAGAGCGTGGAGA

AAGTATCA 1 3+ 3+ 2+ + − VBmut4 CAAAAGAGCGTGG

GAAAAGTATCA 1 3+ 3+ 2+ + − VBmut5 CAAAAGAGCG

GGAGAAAAGTATCA 1 3+ 3+ 2+ + − VBmut6 CAAAAGA

CGTGGAGAAAAGTATCA 1 3+ 3+ 2+ + − VBmut7 CAAA

GAGCGTGGAGAAAAGTATCA 1 3+ 3+ 2+ + − VBmut8 C

AAAGAGCGTGGAGAAAAGTATCA 1 3+ 3+ 2+ + − VBmut9 CAAAAGAGCGTGGAGA

AAGTA

CA 2 3+ 3+ 2+ + − VBmut10 CAAAAGAGCG

GGAGA

AAGTATCA 2 3+ 3+ 2+ + − VBmut11 CAAA

GAGCG

GGAGAAAAGTATCA 2 3+ 3+ 2+ + − VBmut12 CAAA

GAGCGTGG

GAAAAGTA

CA 3 3+ 3+ 2+ + − VBmut13 CAAA

GAGCG

GGAGA

AAGTA

CA 4 3+ 2+ + − − ¹All PCR tests were performed with SEQ ID NO: 145 without modification combined with SEQ ID NO: 146 or 13 modified versions of SEQ ID NO: 146. Boxed nucleotides indicate changes in SEQ ID NO: 146. All SEQ ID NOs. are from U.S. Pat No. 6,001,564. ²The tests with S. epidermidis were performed by using an annealing temperature of 55° C. with 1, 0.1 and 0.01 ng of purified genomic DNA or at 50° C. with 1 ng of purified genomic DNA. ³The tests with S. aureus were performed only at 50° C. with 1 ng of genomic DNA. ⁴The intensity of the positive amplification signal was quantified as follows: 3+ = strong signal, 2+ = intermediate signal and + = weak signal.

TABLE 24 Effect of the primer length on the efficiency of the PCR amplification¹: Example with the AT-rich SEQ ID NO: 145² and SEQ ID NO: 146² from S. epidermidis. Staphylococcus Staphylo- epidermidis ³ Staphylo- coccus Staphylo- Staphylo- ATCC 14990 coccus haemo- coccus coccus Length 45° C. 55° C. aureus ⁴ lyticus capitis warneri Primer Sequence (nt) 1 0.1 0.01 1 0.1 0.01 45 55 45 55 45 55 45 55 VBsep301 ATATCATCAAAAAGTTGGCGAACCTTTTCA 30 NT NT NT 4+ 3+ 2+ NT − NT − NT − NT − VBsep302 AATTGCAAAAGAGCGTGGAGAAAAGTATCA 30 SEQ ID ATCAAAAAGTTGGCGAACCTTTTCA 25  4+⁵ 3+ 2+ 4+ 3+ 2+ − − − − + − − − NO: 145 SEQ ID CAAAAGAGCGTGGAGAAAAGTATCA 25 NO: 146 VBsep201 AAAGTTGGCGAACCTTTTCA 20 NT NT NT 4+ 3+ 2+ NT − NT − NT − NT − VBsep202 GAGCGTGGAGAAAAGTATCA 20 VBsep171 GTTGGCGAACCTTTTCA 17 4+ 3+ 2+ 3+ 2+ + − − − − − − − − VBsep172 CGTGGAGAAAAGTATCA 17 VBsep151 TGGCGAACCTTTTCA 15 3+ 2+ + − − − − − − − − − − − VBsep152 TGGAGAAAAGTATCA 15 ¹All PCR tests were performed using an annealing temperature of 45 or 55° C. and 30 cycles of amplification. ²All SEQ ID NOs. in this Table are from U.S. pat. No. 6,001,546. ³The tests with S. epidermidis were made with 1, 0.1 and 0.01 ng of purified genomic DNA. ⁴The tests with all other bacterial species were made only with 1 ng of purified genomic DNA. ⁵The intensity of the positive amplification signal was quantified as follows: 4+ = very strong signal, 3+ = strong signal, 2+ = intermediate signal and + = weak signal. NT = not tested.

TABLE 25 Effect of the primer length on the efficiency of the PCR amplification¹: Example with the GC-rich SEQ ID NO: 83² and SEQ ID NO: 84² from P. aeruginosa. Pseudomonas aeruginosa ³ Length ATCC 35554 Pseudomonas Burkholderia Primer Sequence (nt) 1 0.1 0.01 fluorescens ⁴ cepacia SEQ ID NO 83 CGAGCGGG 19  2+⁵ + − − − TGGTGTTCATC SEQ ID NO 84 CAAGTCGT 19 CGTCGGAGGGA Pse554-16a CGAGCGGG 16 2+ + − − − TGGTGTTC Pse674-16a GTCGTCGT 16 CGGAGGGA Pse554-13b GCGGGTGG 13 2+ + − − − TGTTC Pse674-13a GTCGTCGG 13 AGGGA Shewanella Stenotrophomonas Neisseria Haemophilus Primer putida maltophilia meningitidis parahaemolyticus SEQ ID NO 83 − − − − SEQ ID NO 84 Pse554-16a − − − − Pse674-16a Pse554-13b − − − − Pse674-13a ¹All PCR tests were performed using an annealing temperature of 55° C. and 30 cycles of amplification. ²All SEQ ID NOs. in this Table are from U.S. Pat. No. 6,001,546. ³The tests with P. aeruginosa were made with 1, 0.1 and 0.01 ng of purified genomic DNA. ⁴The tests with all other bacterial species were made only with 1 ng of purified genomic DNA. ⁵The intensity of the positive amplification signal was quantified as follows: 2+ = strong signal and + = moderately strong signal.

TABLE 26 Sequences used for the consensus of the vanA gene GenBank Organism access number Source E. faecium M97297 E. faecium AX111560 Sequence 2293 of patent WO0123604 E. faecium AX085668 Sequence 21 of patent WO0112803 E. faecium AX085648 Sequence 1 of patent WO0112803 E. faecium AX110408 Sequence 1141 of Patent WO0123604 E. faecium AX110406 Sequence 1139 of patent WO0123604 E. faecium AX110320 Sequence 1053 of patent WO0123604 E. faecium AX110319 Sequence 1052 of patent WO0123604 E. faecium AX110318 Sequence 1051 of patent WO0123604 E. faecium AX110316 Sequence 1049 of patent WO0123604 E. faecalis AX110321 Sequence 1054 of patent WO0123604 E. gallinarum AX110317 Sequence 1050 of patent WO0123604 E. gallinarum AX110322 Sequence 1055 of patent WO0123604 E. flavescens AX110324 Sequence 1057 of patent WO0123604 S. aureus AE017171.1 Direct deposit to NCBI (VRSA)

TABLE 27 Sequences used for the consensus of vanB gene Organism GenBank access number Source E. faecium SLH475 AF310954.1 Tn5382 transposon ligase VanB2 (vanB2) gene E. faecium UI709 AY145441.1 D-alanine:D-lactate ligase (vanB2) E. faecium VRE-1 AF310953.1 Tn5382 ligase VanB2 (vanB2) gene E. faecium U94526.1 vancomycin resistance protein B (vanB) gene, E. faecium AJ306727.1 plasmid pVREM3123/00 partial vanHB gene and partial vanB2 gene E. faecium AJ306726.1 plasmid pVREM2497/00 partial vanHB gene and partial vanB2 gene E. faecium Z83305.1 vanB2, vanHB2 and vanXB2 genes E. faecium Z83305.1 vanB2, vanHB2 and vanXB2 genes E. faecium CG4248 AF310957.1 transposon Tn5382 ligase VanB2 (vanB2) gene, E. faecalis L15304.1 vancomycin resistance vanB2 gene E. faecalis U35369.1 vancomycin resistance genes, response regulator (vanRB), protein histidine kinase (vanSB), D,D-carboxypeptidase (vanYB), putative D-2-hydroxyacid dehydrogenase (vanHB), D-Ala:D-Lac ligase (vanB), and putative D,D-dipeptidase (vanXB) genes E. faecalis U00456.1 vanB gene E. faecalis L06138.1 VANB gene E. faecalis U72704.1 vancomycin resistance protein (vanB) gene E. faecalis T4059 AF310955.1 transposon Tn5382 ligase VanB2 (vanB2) gene E. faecalis L15304.1 vancomycin resistance vanB2 gene E. faecalis T4059 AF310955.1 transposon Tn5382 ligase VanB2 (vanB2) gene E. faecalis AF192329.1 transposon Tn1549, complete sequence S. bovis biotype II Z70527.1 partial vanB2 gene S. lutetiensis strain 5-F9 AY035703.1 Tn5382-like transposon ligase VanB2 (vanB2) gene *Deposited directly to NCBI

TABLE 28 Number of positive assay results out of five in VanR Assay. DNA copies number E. faecium E. faecalis 0.5 2 2 2.5 5 3 5 5 4 10 5 5 20 5 5

TABLE 29 First list of exemplary strains tested with VanR assay. ATCC or Ref. No Strains number 1 Enterococcus casseliflavus 25788 2 Enterococcus cecorum 43198 3 Enterococcus columbae 51263 4 Enterococcus malodoratus 43197 5 Enterococcus mundtii 43186 6 Enterococcus pseudoavium 49372 7 Enterococcus raffinosus 49427 8 Enterococcus dispar 51266 9 Enterococcus durans 19432 10 Enterococcus faecalis 19433 11 Enterococcus faecalis 29212 12 Enterococcus faecalis R830 13 Enterococcus faecium 19434 14 Enterococcus faecium N97-330 15 Enterococcus flavescens 49996 16 Enterococcus gallinarum 49573 17 Enterococcus saccharolyticus 43076 18 Enterococcus sulfureus 49903 19 Enterococcus faecium (vanD) CCRI-14889 20 Enterococcus faecium (vanD) CCRI-14889 21 Enterococcus faecalis (vanE) CCRI-1908 22 Enterococcus faecalis (vanE) CCRI-1908 23 Enterococcus faecalis (vanG) CCRI-12848 24 Enterococcus faecalis (vanG) CCRI-12848

TABLE 30 Second list of exemplary strains tested with VanR assay ATCC or Ref. No Strains number 1 Acinetobacter twoffii CDCF 3697 2 Aeromonas hydrophila 7966 3 Bacteroides fragilis 25285 4 Bacillus cereus 13472 5 Bifidobacterium breve 15700 6 Candida albicans 10231 7 Clostridium difficile 9689 8 Clostridium perfringens 13124 9 Corynebacterium bovis 7715 10 Escherichia coli 25922 11 Escherichia coli 23511 12 Fusobacterium nucleatum 10953 13 Gardnerella vaginalis 14019 14 Klebsiella oxytoca 33496 15 Klebsiella pneumoniae 13883 16 Listeria monocytogenes L 374 17 Morganella morganii subsp. morganii 25830 18 Peptostreptococcus anaerobius 27337 19 Peptostreptococcus asaccharolyticus LSPQ 2639 20 Porphyromonas asaccharolytica 25260 21 Prevotella melaninogenica 25845 22 Propionibacterium acnes 6919 23 Staphylococcus epidermidis 14990 24 Stenotrophomonas maltophilia 13637

TABLE 31 Third list of exemplary strains tested with VanR assay. ATCC or Ref. No Strains number 1 Abiotrophia defectiva 49176 2 Acinetobacter baumannii 19606 3 Actinomyces pyogenes 19411 4 Citrobacter braakii 43162 5 Citrobacter koseri 27028 6 Corynebacterium genitalium LSPQ 3583 7 Enterobacter cloacae 13047 8 Hafnia alvei 13337 9 Homo sapiens 2.16 10 Lactobacillus acidophilus 4356 11 Lactobacillus gasseri 33323 12 Mobiluncus curtisii subsp. holmesii 35242 13 Neisseria gonorrhoeae 35201 14 Pantoea agglomerans 27155 15 Pseudomonas aeruginosa 35554 16 Salmonella enterica subsp. Arizonae 13314 17 Salmonella enterica subsp. Enterica 7001 18 Salmonella typhimurium 14028 19 Shigella flexneri 12022 20 Shigella sonnei 29930 21 Staphylococcus aureus 43300 22 Streptococcus anginosus 33397 23 Streptococcus bovis 33317 24 Vibrio cholerae 25870 25 Yersinia enterocolitica subs. enterolitica 23715

TABLE 32 Vancomycin resistant strains tested with VanR assay at 10⁵ CFU/rx. ATCC or Ref. No Strains Resistance gene number 1-2 Enterococcus casseliflavus vanC2 25788 (10⁴ CFU/rx) 3-4 Enterococcus casseliflavus vanC2 25788 5-6 Enterococcus faecalis vanG CCRI-12849 7-8 Enterococcus faecium vanD R832  9-10 Enterococcus faecium vanD2 CCRI-15140 11-12 Enterococcus faecium vanD CCRI-2062 13-14 Enterococcus faecium vanD CCRI-8824 15-16 Enterococcus gallinarum vanC CCRI-9133 17-18 Enterococcus gallinarum vanC CCRI-9131 19-20 Enterococcus gallinarum vanA and vanC1 CCRI-1561

TABLE 33 Composition of premix (PM) CONCENTRATION IN FRESHLY PREPARED MIX COMPONENT (28.8 μL FINAL VOLUME) FastStart Taq DNA Polymerase 0.060 U/μL MgCl₂ 3.010 mM Tris 100.333 mM KCl 10.033 mM (NH₄)₂SO₄ 5.017 mM dNTPs 200.667 μM Primer vanA649 (SEQ ID NO: 1090) 0.120 μM Primer vanA754 (SEQ ID NO: 1091) 0.101 μM Primer vanB626 (SEQ ID NO: 2298) 0.702 μM Primer vanB774 (SEQ ID NO: 1096) 0.702 μM Probe VanA-B5c-A0 (SEQ ID NO: 2299) 0.120 μM Probe Van8-850-F0 (SEW ID NO: 2300) 0.351 μM Probe Sign-B4-B0 (SEQ ID NO: 2301) 0.201 μM pERVd Internal control (SEQ ID NO: 3.582 copies/μL (usual) 2302) S. epidermidis DNA 895.836 copies/μL BSA 0.301 mg/mL Trehalose 4.014% *These components were added following Table 21

TABLE 34 Composition of final mix (MM) Sign-B4 VanA- VanB-B50 IC (SEQ (SEQ ID NO: B5c (SEQ ID (SEQ ID NO: ID NO: n 2301) NO: 2299) 2300) 2302) Specimen MM1-a 10 x DNA³ MM1-b 5 x x¹ TE 1X MM2-a 10 X DNA³ MM2-b 5 X x¹ TE 1X MM3-a 10 x DNA³ MM3-b 5 X x¹ TE 1X MM4-std 15 x X X x² DNA⁴/TE 1X ¹At 100 times the usual concentration ²At usual concentration ³At 25/50 VanA/VanB DNA copies ⁴At 1 ng/rx VanA/VanB DNA copies

TABLE 35 Positive results obtained in indicated beacon channel Sign-B4 VanB-B50 (SEQ ID NO: VanA-B5 (SEQ (SEQ ID NO: 2301) ID NO: 2299)c 2300) TET FAM Texas Red Target MM1-a 0/5 — — Efm 0/5 — — Efs MM1-b 5/5 — — IC MM2-a — 5/5 — Efm — 0/5 — Efs MM2-b — 0/5 — IC MM3-a — — 0/5 Efm — — 5/5 Efs MM3-b — — 0/5 IC MM4-std 5/5 5/5 0/5 Efm 5/5 0/5 5/5 Efs 5/5 0/5 0/5 IC

TABLE 36 List of enterococcal strains from different locations around the world tested with VanR assay (dilutions 10⁻³). No Strains Reference number Location vanA CT vanB CT 1 Enterococcus faecalis CCRI-1471 Texas, USA 29.91 — 2 Enterococcus faecalis CCRI-1528 Quebec, CAN 27.05 — 3 Enterococcus faecalis CCRI-9741 USA — 31.05 4 Enterococcus gallinarum CCRI-1568 Quebec, CAN 28.60 — 5 Enterococcus faecium CCRI-9911 Taiwan, China — 31.96 6 Enterococcus faecalis  725 Israel — 31.55 7 Enterococcus faecalis  1435 Brazil 28.28 — 8 Enterococcus faecium  6169 Italy 31.63 — 9 Enterococcus gallinarum CCRI-9737 Norway — 29.50 10 Enterococcus faecalis CCRI-9738 Germany — 31.35 11 Enterococcus faecium CCRI-9740 Germany — 29.41 12 Enterococcus faecalis 13024 Germany 27.49 — 13 Enterococcus faecalis CCRI-9739 Germany — 31.00 14 Enterococcus faecium CCRI-9733 USA — 31.93 15 Enterococcus faecium  1585 Argentina 29.00 — 16 Enterococcus faecium  715 Sweden — 30.87 17 Enterococcus faecalis CCRI-9954 Netherlands — 31.83 18 Enterococcus faecium CCRI-1482 Toronto, CAN 29.40 — *All strains gave vanA or vanB positive PCR results.

TABLE 37 List of resistant non enterococcal strains (vanB genotype) tested with VanR assay. Reference Texas Red CT No Strains number (cycles) 1 Clostridium innocuum CCRI-9927 29.6 2 Clostridium sp. IDI-1987 31.9 3 Clostridium sp. CCRI-9929 32.5 4 Clostridium symbosium CCRI-9928 31.6 5 Eggerthella lenta CCRI-9926 32.4 *All strains gave vanB positive PCR results.

TABLE 38 VanR Assay Formulation Concentration of Concentration of components at components at final volume (28 μL) final volume (28.8 μL) Raw Material Lyophilized Fresh FastStart Taq DNA Polymerase 0..060 U/μL¹ 0.060 U/μL¹ MgCl₂ 3.000 mM² 3.010 mM² Tris 100.000 mM (pH 8.3)² 100.333 mM (pH 8.3)² KCl 10.000 mM² 10.033 mM² (NH₄)₂S0₄ 5.000 mM² 5.017 mM² dNTP 200.000 μM 200.667 μM Primer VanA 649 (SEQ ID NO: 1090) 0.120 μM 0.120 μM Primer Van A 754 (SEQ ID NO: 1091) 0.100 μM 0.101 μM Primer Van B 626 (SEQ ID NO: 2298) 0.700 μM 0.702 μM Primer van B 774 (SEQ ID NO: 1096) 0.700 μM 0.702 μM Probe VanA-B5c-A0 (SEQ ID NO: 2299) 0.120 μM 0.120 μM Probe VanB-B50-F0 (SEQ ID NO: 2300) 0.350 μM 0.351 μM Probe Sign-B4-B0 (SEQ ID NO: 2301) 0.200 μM 0.201 μM Internal control pERVd (SEQ ID NO: 2302) 3.570 copies/μL 3.582 copies/μL S. epidermidis DNA 892.857 copies/μL³ 895.836 copies/μL³ BSA 0.300 mg/mL 0.301 mg/mL Trehalose 4.000% 4.014%

Annex I: Specific and ubiquitous primers for nucleic acid amplification (tuf sequences). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial species: Acinetobacter baumannii 1692 5′-GGT GAG AAC TGT GGT ATC TTA CTT 1 478-501 1693^(a) 5′-CAT TTC AAC GCC TTC TTT CAA CTG 1 691-714 Bacterial species: Chlamydia pneumoniae 630 5′-CGG AGC TAT CCT AGT CGT TTC A 20 2-23 629^(a) 5′-AAG TTC CAT CTC AAC AAG GTC AAT A 20 146-170 2085 5′-CAA ACT AAA GAA CAT ATC TTG CTA 20 45-68 2086^(a) 5′-ATA TAA TTT GCA TCA CCT TCA AG 20 237-259 2087 5′-TCA GCT CGT GGG ATT AGG AGA G 20 431-452 2088^(a) 5′-AGG CTT CAC GCT GTT AGG CTG A 20 584-605 Bacterial species: Chlamydia trachomatis 554 5′-GTT CCT TAC ATC GTT GTT TTT CTC 22 82-105 555^(a) 5′-TCT CGA ACT TTC TCT ATG TAT GCA 22 249-272 Parasitical species: Cryptosporidium parvum 798 5′-TGG TTG TCC CAG CCG ATC GTT T 865 158-179 804^(a) 5′-CCT GGG ACG GCC TCT GGC AT 865 664-683 799 5′-ACC TGT GAA TAC AAG CAA TCT 865 280-300 805^(a) 5′-CTC TTG TCC ATC TTA GCA GT 865 895-914 800 5′-GAT GAA ATC TTC AAC GAA GTT GAT 865 307-330 806^(a) 5′-AGC ATC ACC AGA CTT GAT AAG 865 946-966 801 5′-ACA ACA CCG AGA AGA TCC CA 865 353-372 803^(a) 5′-ACT TCA GTG GTA ACA CCA GC 865 616-635 802 5′-TTG CCA TTT CTG GTT TCG TT 865 377-396 807^(a) 5′-AAA GTG GCT TCA AAG GTT GC 865 981-1000 Bacterial species: Enterococcus faecium 1696 5′-ATG TTC CTG TAG TTG CTG GA 64 189-208 1697^(a) 5′-TTT CTT CAG CAA TAC CAA CAA C 64 422-443 Bacterial species: Klebsiella pneumoniae 1329 5′-TGT AGA GCG CGG TAT CAT CAA AGT A 103 352-377 1330^(a) 5′-AGA TTC GAA CTT GGT GTG CGG G 103 559-571 ^(a)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial species: Mycoplasma pneumoniae 2093 5′-TGT TGG CAA TCG AAG ACA CC 2097^(a) 635-654 2094^(b) 5′-TTC AAT TTC TTG ACC TAC TTT CAA 2097^(a) 709-732 Bacterial species: Neisseria gonorrhoeae 551 5′-GAA GAA AAA ATC TTC GAA CTG GCT A 126 256-280 552^(b) 5′-TAC ACG GCC GGT GAC TAC G 126 378-396 2173 5′-AAG AAA AAA TCT TCG AAC TGG CTA 126 257-280 2174^(b) 5′-TCT ACA CGG CCG GTG 126 384-398 2175 5′-CCG CCA TAC CCC GTT T 126 654-669 2176^(b) 5′-CGG CAT TAC CAT TTC CAC ACC TTT 126 736-759 Bacterial species: Pseudomonas aeruginosa 1694 5′-AAG GCA AGG ATG ACA ACG GC 153 231-250 1695^(b) 5′-ACG ATT TCC ACT TCT TCC TGG 153 418-438 Bacterial species: Streptococcus agalactiae 549 5′-GAA CGT GAT ACT GAC AAA CCT TTA 207-210^(c) 308-331^(d) 550^(b) 5′-GAA GAA GAA CAC CAA CGT TG 207-210^(c) 520-539^(d) Bacterial species: Streptococcus pyogenes 999 5′-TTG ACC TTG TTG ATG ACG AAG AG 1002 143-165 1000^(b) 5′-TTA GTG TGT GGG TTG ATT GAA CT 1002 622-644 1001 5′-AAG AGT TGC TTG AAT TAG TTG AG 1002 161-183 1000^(b) 5′-TTA GTG TGT GGG TTG ATT GAA CT 1002 622-644 Parasitical species: Trypanosoma brucei 820 5′-GAA GGA GGT GTC TGC TTA CAC 864 513-533 821^(b) 5′-GGC GCA AAC GTC ACC ACA TCA 864 789-809 820 5′-GAA GGA GGT GTC TGC TTA CAC 864 513-533 822^(b) 5′-CGG CGG ATG TCC TTA ACA GAA 864 909-929 ^(a)Sequence from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(c)These sequences were aligned to derive the corresponding primer. ^(d)The nucleotide positions refer to the S. agalactiae tuf sequence fragment (SEQ ID NO. 209). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Parasitical species: Trypanosoma cruzi 794 5′-GAC GAC AAG TCG GTG AAC TT 840-842^(a) 281-300^(c) 795^(b) 5′-ACT TGC ACG CGA TGT GGC AG 840-842^(a) 874-893^(c) Bacterial genus: Clostridium sp. 796 5′-GGT CCA ATG CCW CAA ACW AGA 32,719-724, 32-52^(d) 736^(a) 797^(b) 5′-CAT TAA GAA TGG YTT ATC TGT SKC TCT 32, 719-724, 320-346^(d) 736^(a) 808 5′-GCI TTA IWR GCA TTA GAA RAY CCA 32, 719-724, 224-247^(d) 736^(a) 809^(b) 5′-TCT TCC TGT WGC AAC TGT TCC TCT 32, 719-724, 337-360^(d) 736^(a) 810 5′-AGA GMW ACA GAT AAR SCA TTC TTA 32, 719-724, 320-343^(d) 736^(a) 811^(b) 5′-TRA ART AGA ATT GTG GTC TRT ATC C 32, 719-724, 686-710^(d) 736^(a) Bacterial genus: Corynebacterium sp. 545 5′-TAC ATC CTB GTY GCI CTI AAC AAG TG 34-44, 662^(a) 89-114^(e) 546^(b) 5′-CCR CGI CCG GTR ATG GTG AAG AT 34-44, 662^(a) 350-372^(e) Bacterial genus: Enterococcus sp. 656 5′-AAT TAA TGG CTG CAG TTG AYG A 58-72^(a) 273-294^(f) 657^(b) 5′-TTG TCC ACG TTC GAT RTC TTC A 58-72^(a) 556-577^(f) 656 5′-AAT TAA TGG CTG CAG TTG AYG A 58-72^(a) 273-294^(f) 271^(b) 5′-TTG TCC ACG TTG GAT RTC TTC A 58-72^(a) 556-577^(f) 1137 5′-AAT TAA TGG CTG CWG TTG AYG AA 58-72^(a) 273-295^(f) 1136^(b) 5′-ACT TGT CCA CGT TSG ATR TCT 58-72^(a) 559-579^(f) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(c) The nucleotide positions refer to the T. cruzi tuf sequence fragment (SEQ ID NO. 842). ^(d) The nucleotide positions refer to the C. perfringens tuf sequence fragment (SEQ ID NO. 32). ^(e) The nucleotide positions refer to the C. diphtheriae tuf sequence fragment (SEQ ID NO. 662). ^(f) The nucleotide positions refer to the E. durans tuf sequence fragment (SEQ ID NO. 61). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial genus: Legionella sp. 2081 5′-GRA TYR TYA AAG TTG GTG AGG AAG 111-112^(a) 411-434^(b) 2082^(c) 5′-CMA CTT CAT CYC GCT TCG TAC C 111-112^(a) 548-569^(b) Bacterial genus: Staphylococcus sp. 553 5′-GGC CGT GTT GAA CGT GGT CAA ATC A 176-203^(a) 313-337^(d) 575^(c) 5′-TIA CCA TTT CAG TAC CTT CTG GTA A 176-203^(a) 653-677^(d) 553 5′-GGC CGT GTT GAA CGT GGT CAA ATC A 176-203^(a) 313-337^(d) 707^(c) 5′-TWA CCA TTT CAG TAC CTT CTG GTA A 176-203^(a) 653-677^(d) Bacterial genus: Streptococcus sp. 547 5′-GTA CAG TTG CTT CAG GAC GTA TC 206-231^(a) 372-394^(e) 548^(c) 5′-ACG TTC GAT TTC ATC ACG TTG 206-231^(a) 548-568^(e) Fungal genus: Candida sp. 576 5′-AAC TTC RTC AAG AAG GTY GGT TAC AA 407-426, 332-357^(f) 428-432^(a) 632^(c) 5′-CCC TTT GGT GGR TCS TKC TTG GA 407-426, 791-813^(f) 428-432^(a) 631 5′-CAG ACC AAC YGA IAA RCC ATT RAG AT 407-426, 523-548^(f) 428-432^(a) 632^(c) 5′-CCC TTT GGT GGR TCS TKC TTG GA 407-426, 791-813^(f) 428-432^(a) 633 5′-CAG ACC AAC YGA IAA RCC ITT RAG AT 407-426, 523-548^(f) 428-432^(a) 632^(c) 5′-CCC TTT GGT GGR TCS TKC TTG GA 407-426, 791-813^(f) 428-432^(a) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the L. pneumophila tuf sequence fragment (SEQ ID NO. 112). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)The nucleotide positions refer to the S. aureus tuf sequence fragment (SEQ ID NO. 179). ^(e)The nucleotide positions refer to the S. agalactiae tuf sequence fragment (SEQ ID NO. 209). ^(f)The nucleotide positions refer to the C. albicans tuf(EF-1) sequence fragment (SEQ ID NO. 408). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Fungal genus: Cryptococcus sp. 1971 5′-CYG ACT GYG CCA TCC TYA TCA 434, 623, 1281, 150-170^(b) 1985, 1986^(a) 1973^(c) 5′-RAC ACC RGI YTT GGW ITC CTT 434, 623, 1281, 464-484^(b) 1985, 1986^(a) 1972 5′-MGI CAG CTC ATY ITT GCW KSC 434, 623, 1281, 260-280^(b) 1985, 1986^(a) 1973^(c) 5′-RAC ACC RGI YTT GGW ITC CTT 434, 623, 1281, 464-484^(b) 1985, 1986^(a) Parasitical genus: Entamoeba sp. 703 5′-TAT GGA AAT TCG AAA CAT CT 512 38-57 704^(c) 5′-AGT GCT CCA ATT AAT GTT GG 512 442-461 703 5′-TAT GGA AAT TCG AAA CAT CT 512 38-57 705^(c) 5′-GTA CAG TTC CAA TAC CTG AA 512 534-553 703 5′-TAT GGA AAT TCG AAA CAT CT 512 38-57 706^(c) 5′-TGA AAT CTT CAC ATC CAA CA 512 768-787 793 5′-TTA TTG TTG CTG CTG GTA CT 512 149-168 704^(c) 5′-AGT GCT CCA ATT AAT GTT GG 512 442-461 Parasitical genus: Giardia sp. 816 5′-GCT ACG ACG AGA TCA AGG GC 513 305-324 819^(c) 5′-TCG AGC TTC TGG AGG AAG AG 513 895-914 817 5′-TGG AAG AAG GCC GAG GAG TT 513 355-374 818^(c) 5′-AGC CGG GCT GGA TCT TCT TC 513 825-844 Parasitical genus: Leishmania sp. 701 5′-GTG TTC ACG ATC ATC GAT GCG 514-526^(a) 94-114^(d) 702^(c) 5′-CTC TCG ATA TCC GCG AAG CG 514-526^(a) 913-932^(d) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the C. neoformans tuf (EF-1) sequence fragment (SEQ ID NO. 623). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)The nucleotide positions refer to the L. tropica tuf(EF-1) sequence fragment (SEQ ID NO. 526). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Parasitical genus: Trypanosoma sp. 823 5′-GAG CGG TAT GAY GAG ATT GT 529, 840-842, 493-512^(b) 864^(a) 824^(c) 5′-GGC TTC TGC GGC ACC ATG CG 529, 840-842, 1171-1190^(b) 864^(a) Bacterial family: Enterobacteriaceae 933 5′-CAT CAT CGT ITT CMT GAA CAA RTG 78, 103, 146, 390-413^(d) 168, 238, 698^(a) 934^(c) 5′-TCA CGY TTR RTA CCA CGC AGI AGA 78, 103, 146, 831-854^(d) 168, 238, 698^(a) Bacterial family: Mycobacteriaceae 539 5′-CCI TAC ATC CTB GTY GCI CTI AAC AAG 122 85-111 540^(c) 5′-GGD GCI TCY TCR TCG WAI TCC TG 122 181-203 Bacterial group: Escherichia coli and Shigella 1661 5′-TGG GAA GCG AAA ATC CTG 1668^(e) 283-300 1665^(c) 5′-CAG TAC AGG TAG ACT TCT G 1668^(e) 484-502 Bacterial group: Pseudomonads group 541 5′-GTK GAA ATG TTC CGC AAG CTG CT 153-155^(a) 476-498^(f) 542^(c) 5′-CGG AAR TAG AAC TGS GGA CGG TAG 153-155^(a) 679-702^(f) 541 5′-GTK GAA ATG TTC CGC AAG CTG CT 153-155^(a) 476-498^(f) 544^(c) 5′-AYG TTG TCG CCM GGC ATT MCC AT 153-155^(a) 749-771^(f) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the T. brucei tuf (EF-1) sequence fragment (SEQ ID NO. 864). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)The nucleotide positions refer to the E. coli tuf sequence fragment (SEQ ID NO. 698). ^(e)Sequence from databases. ^(f)The nucleotide positions refer to the P. aeruginosa tuf sequence fragment (SEQ ID NO. 153). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Parasitical group: Trypanosomatidae family 923 5′-GAC GCI GCC ATC CTG ATG ATC 511, 514-526, 166-188^(b) 529, 840-842, 864^(a) 924^(c) 5′-ACC TCA GTC GTC ACG TTG GCG 511, 514-526, 648-668^(b) 529, 840-842, 864^(a) 925 5′-AAG CAG ATG GTT GTG TGC TG 511, 514-526, 274-293^(b) 529, 840-842, 864^(a) 926^(c) 5′-CAG CTG CTC GTG GTG CAT CTC GAT 511, 514-526, 676-699^(b) 529, 840-842, 864^(a) 927 5′-ACG CGG AGA AGG TGC GCT T 511, 514-526, 389-407^(b) 529, 840-842, 864^(a) 928^(c) 5′-GGT CGT TCT TCG AGT CAC CGC A 511, 514-526, 778-799^(b) 529, 840-842, 864^(a) Universal primers (bacteria) 636 5′-ACT GGY GTT GAI ATG TTC CGY AA 7, 54, 78, 470-492^(d) 100, 103, 159, 209, 224, 227^(b) 637^(c) 5′-ACG TCA GTI GTA CGG AAR TAG AA 7, 54, 78, 692-714^(d) 100, 103, 159, 209, 224, 227^(b) 638 5′-CCA ATG CCA CAA ACI CGT GAR CAC AT 7, 54, 78, 35-60^(e) 100, 103, 159, 209, 224, 227^(b) 639^(c) 5′-TTT ACG GAA CAT TTC WAC ACC WGT IAC A 7, 54, 78, 469-496^(e) 100, 103, 159, 209, 224, 227^(b) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the L. tropica tuf (EF-1) sequence fragment (SEQ ID NO. 526). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)The nucleotide positions refer to the E. coli tuf sequence fragment (SEQ ID NO. 78). ^(e)The nucleotide positions refer to the B. cereus tuf sequence fragment (SEQ ID NO. 7). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Universal primer (bacteria) (continued) 643 5′-ACT GGI GTI GAR ATG TTC CGY AA 1, 3, 4, 7, 12, 470-492^(b) 13, 16, 49, 54, 72, 78, 85, 88, 91, 94, 98, 103, 108, 112, 115, 116, 120, 121, 126, 128, 134, 136, 146, 154, 159, 179, 186, 205, 209, 212, 224, 238^(a) 644^(c) 5′-ACG TCI GTI GTI CKG AAR TAG AA same as SEQ 692-714^(b) ID NO. 643 643 5′-ACT GGI GTI GAR ATG TTC CGY AA 1, 3, 4, 7, 12, 470-492^(b) 13, 16, 49, 54, 72, 78, 85, 88, 91, 94, 98, 103, 108, 112, 115, 116, 120, 121, 126, 128, 134, 136, 146, 154, 159, 179, 186, 205, 209, 212, 224, 238^(a) 645^(c) 5′-ACG TCI GTI GTI CKG AAR TAR AA same as SEQ 692-714^(b) ID NO. 643 646 5′-ATC GAC AAG CCI TTC YTI ATG SC 2, 13, 82 317-339^(d) 122, 145^(a) 647^(c) 5′-ACG TCC GTS GTR CGG AAG TAG AAC TG 2, 13, 82 686-711^(d) 122, 145^(a) 646 5′-ATC GAC AAG CCI TTC YTI ATG SC 2, 13, 82 317-339^(d) 122, 145^(a) 648^(c) 5′-ACG TCS GTS GTR CGG AAG TAG AAC TG 2, 13, 82 686-711^(d) 122, 145^(a) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the E. coli tuf sequence fragment (SEQ ID NO. 78). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)The nucleotide positions refer to the A. meyeri tuf sequence fragment (SEQ ID NO. 2) Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Universal primer (bacteria) (continued) 649 5′-GTC CTA TGC CTC ARA CWC GIG AGC AC 8, 86, 141, 143^(a) 33-58^(b) 650^(c) 5′-TTA CGG AAC ATY TCA ACA CCI GT 8, 86, 141, 143^(a) 473-495^(b) 636 5′-ACT GGY GTT GAI ATG TTC CGY AA 8, 86, 141, 143^(a) 473-495^(b) 651^(c) 5′-TGA CGA CCA CCI TCY TCY TTY TTC A 8, 86, 141, 143^(a) 639-663^(b) Universal primers (fungi) 1974 5′-ACA AGG GIT GGR MSA AGG AGA C 404, 405, 433, 443-464^(d) 445, 898, 1268, 1276, 1986^(a) 1975^(c) 5′-TGR CCR GGG TGG TTR AGG ACG 404, 405, 433, 846-866^(d) 445, 898, 1268, 1276, 1986^(a) 1976 5′-GAT GGA YTC YGT YAA ITG GGA 407-412, 286-306^(e) 414-426, 428-431, 439, 443, 447, 448, 622, 624, 665, 1685, 1987-1990^(a) 1978^(c) 5′-CAT CIT GYA ATG GYA ATC TYA AT same as SEQ 553-575^(e) ID NO. 1976 1977 5′-GAT GGA YTC YGT YAA RTG GGA same as SEQ 286-306^(e) ID NO. 1976 1979^(c) 5′-CAT CYT GYA ATG GYA ASC TYA AT same as SEQ 553-575^(e) ID NO. 1976 1981 5′-TGG ACA CCI SCA AGI GGK CYG 401-405, 281-301^(d) 433, 435, 436, 438, 444, 445, 449, 453, 455, 457, 779, 781-783, 785, 786, 788-790, 897-903, 1267-1272, 1274-1280, 1282-1287, 1991-1998^(a) 1980^(c) 5′-TCR ATG GCI TCI AIR AGR GTY T same as SEQ 488-509^(d) ID NO. 1981 ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the B. distasonis tuf sequence fragment (SEQ ID NO. 8). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)The nucleotide positions refer to the A. fumigatus tuf (EF-1) sequence fragment (SEQ ID NO. 404). ^(e)The nucleotide positions refer to the C. albicans tuf (EF-1) sequence fragment (SEQ ID NO. 407). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Universal primers (fungi) (continued) 1982 5′-TGG ACA CYI SCA AGI GGK CYG same as SEQ 281-301^(a) ID NO. 1981 1980^(b) 5′-TCR ATG GCI TCI AIR AGR GTY T same as SEQ 488-509^(a) ID NO. 1981 1983 5′-CYG AYT GCG CYA TIC TCA TCA same as SEQ 143-163^(a) ID NO. 1981 1980^(b) 5′-TCR ATG GCI TCI AIR AGR GTY T same as SEQ 488-509^(a) ID NO. 1981 1984 5′-CYG AYT GYG CYA TYC TSA TCA same as SEQ 143-163^(a) ID NO. 1981 1980^(b) 5′-TCR ATG GCI TCI AIR AGR GTY T same as SEQ 488-509^(a) ID NO. 1981 Sequencing primers 556 5′-CGG CGC NAT CYT SGT TGT TGC 668^(c) 306-326 557^(b) 5′-CCM AGG CAT RAC CAT CTC GGT G 668^(c) 1047-1068 694 5′-CGG CGC IAT CYT SGT TGT TGC 668^(c) 306-326 557^(b) 5′-CCM AGG CAT RAC CAT CTC GGT G 668^(c) 1047-1068 664 5′-AAY ATG ATI ACI GGI GCI GCI CAR ATG GA 619^(c) 604-632 652^(b) 5′-CCW AYA GTI YKI CCI CCY TCY CTI ATA 619^(c) 1482-1508 664 5′-AAY ATG ATI ACI GGI GCI GCI CAR ATG GA 619^(c) 604-632 561^(b) 5′-ACI GTI CGG CCR CCC TCA CGG AT 619^(c) 1483-1505 543 5′-ATC TTA GTA GTT TCT GCT GCT GA 607 8-30 660^(b) 5′-GTA GAA TTG AGG ACG GTA GTT AG 607 678-700 658 5′-GAT YTA GTC GAT GAT GAA GAA TT 621 116-138 659^(b) 5′-GCT TTT TGI GTT TCW GGT TTR AT 621 443-465 658 5′-GAT YTA GTC GAT GAT GAA GAA TT 621 116-138 661^(b) 5′-GTA GAA YTG TGG WCG ATA RTT RT 621 678-700 558 5′-TCI TTY AAR TAY GCI TGG GT 665^(c) 157-176 559^(b) 5′-CCG ACR GCR AYI GTY TGI CKC AT 665^(c) 1279-1301 813 5′-AAT CYG TYG AAA TGC AYC ACG A 665^(c) 687-708 559^(b) 5′-CCG ACR GCR AYI GTY TGI CKC AT 665^(c) 1279-1301 ^(a)The nucleotide positions refer to the A. fumigatus tuf (EF-1) sequence fragment (SEQ ID NO. 404). ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(c)Sequences from databases. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Sequencing primers (continued) 558 5′-TCI TTY AAR TAY GCI TGG GT 665^(a) 157-176 815^(b) 5′-TGG TGC ATY TCK ACR GAC TT 665^(a) 686-705 560 5′-GAY TTC ATY AAR AAY ATG ATY AC 665^(a) 289-311 559^(b) 5′-CCG ACR GCR AYI GTY TGI CKC AT 665^(a) 1279-1301 653 5′-GAY TTC ATI AAR AAY ATG AT 665^(a) 289-308 559^(b) 5′-CCG ACR GCR AYI GTY TGI CKC AT 665^(a) 1279-1301 558 5′-TCI TTY AAR TAY GCI TGG GT 665^(a) 157-176 655^(b) 5′-CCR ATA CCI CMR ATY TTG TA 665^(a) 754-773 654 5′-TAC AAR ATY KGI GGT ATY GG 665^(a) 754-773 559^(b) 5′-CCG ACR GCR AYI GTY TGI CKC AT 665^(a) 1279-1301 696 5′-ATI GGI CAY RTI GAY CAY GGI AAR AC 698^(a) 52-77 697^(b) 5′-CCI ACI GTI CKI CCR CCY TCR CG 698^(a) 1132-1154 911 5′-GAC GGM KKC ATG CCG CAR AC 853 22-41 914^(b) 5′-GAA RAG CTG CGG RCG RTA GTG 853 700-720 912 5′-GAC GGC GKC ATG CCG CAR AC 846 20-39 914^(b) 5′-GAA RAG CTG CGG RCG RTA GTG 846 692-712 913 5′-GAC GGY SYC ATG CCK CAG AC 843 251-270 915^(b) 5′-AAA CGC CTG AGG RCG GTA GTT 843 905-925 916 5′-GCC GAG CTG GCC GGC TTC AG 846 422-441 561^(b) 5′-ACI GTI CGG CCR CCC TCA CGG AT 619^(a) 1483-1505 664 5′-AAY ATG ATI ACI GGI GCI GCI CAR ATG GA 619^(a) 604-632 917^(b) 5′-TCG TGC TAC CCG TYG CCG CCA T 846 593-614 ^(a)Sequences from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Sequencing primers (continued) 1221 5′-GAY ACI CCI GGI CAY GTI GAY TT 1230^(a) 292-314 1226^(b) 5′-GTI RMR TAI CCR AAC ATY TC 1230^(a) 2014-2033 1222 5′-ATY GAY ACI CCI GGI CAY GTI GAY TT 1230^(a) 289-314 1223^(b) 5′-AYI TCI ARR TGI ARY TCR CCC ATI CC 1230^(a) 1408-1433 1224 5′-CCI GYI HTI YTI GAR CCI ATI ATG 1230^(a) 1858-1881 1225^(b) 5′-TAI CCR AAC ATY TCI SMI ARI GGI AC 1230^(a) 2002-2027 1227 5′-GTI CCI YTI KCI GAR ATG TTY GGI TA 1230^(a) 2002-2027 1229^(b) 5′-TCC ATY TGI GCI GCI CCI GTI ATC AT 698^(a) 4-29 1228 5′-GTI CCI YTI KCI GAR ATG TTY GGI TAY GC 1230^(a) 2002-2030 1229^(b) 5′-TCC ATY TGI GCI GCI CCI GTI ATC AT 698^(a) 4-29 1999 5′-CAT GTC AAY ATT GGT ACT ATT GGT CAT GT 498-500, 25-53^(d) 502, 505, 506, 508, 619, 2004, 2005^(c) 2000^(b) 5′-CCA CCY TCI CTC AMG TTG AAR CGT T same as SEQ 1133-1157^(d) ID NO. 1999 2001 5′-ACY ACI TTR ACI GCY GCY ATY AC same as SEQ 67-89^(d) ID NO. 1999 2003^(b) 5′-CAT YTC RAI RTT GTC ACC TGG same as SEQ 1072-1092^(d) ID NO. 1999 2002 5′-CCI GAR GAR AGA GCI MGW GGT same as SEQ 151-171^(d) ID NO. 1999 2003^(b) 5′-CAT YTC RAI RTT GTC ACC TGG same as SEQ 1072-1092^(d) ID NO. 1999 ^(a)Sequences from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(c)These sequences were aligned to derive the corresponding primer. ^(d)The nucleotide positions refer to the C. albicans tuf sequence fragment (SEQ ID NO. 2004).

Annex II: Specific and ubiquitous primers for nucleic acid amplification (atpD sequences). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial species: Acinetobacter baumannii 1690 5′-CAG GTC CTG TTG CGA CTG AAG AA 243 186-208 1691^(b) 5′-CAC AGA TAA ACC TGA GTG TGC TTT C 243 394-418 Bacterial species: Bacteroides fragilis 2134 5′-CGC GTG AAG CTT CTG TG 929 184-200 2135^(b) 5′-TCT CGC CGT TAT TCA GTT TC 929 395-414 Bacterial species: Bordetella pertussis 2180 5′-TTC GCC GGC GTG GGC 1672^(c) 544-558 2181^(b) 5′-AGC GCC ACG CGC AGG 1672^(c) 666-680 Bacterial species: Enterococcus faecium 1698 5′-GGA ATC AAC AGA TGG TTT ACA AA 292 131-153 1699^(b) 5′-GCA TCT TCT GGG AAA GGT GT 292 258-277 1700 5′-AAG ATG CGG AAA GAA GCG AA 292 271-290 1701^(b) 5′-ATT ATG GAT CAG TTC TTG GAT CA 292 439-461 Bacterial species: Klebsiella pneumoniae 1331 5′-GCC CTT GAG GTA CAG AAT GGT AAT GAA GTT 317 88-118 1332^(b) 5′-GAC CGC GGC GCA GAC CAT CA 317 183-203 ^(a)These sequences were aligned to derive the corresponding primer. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(c)Sequence from databases. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial species: Streptococcus agalactiae 627 5′-ATT GTC TAT AAA AAT GGC GAT AAG TC 379-383^(a) 42-67^(b) 625^(c) 5′-CGT TGA AGA CAC GAC CCA AAG TAT CC 379-383^(a) 206-231^(b) 628 5′-AAA ATG GCG ATA AGT CAC AAA AAG TA 379-383^(a) 52-77^(b) 625^(c) 5′-CGT TGA AGA CAC GAC CCA AAG TAT CC 379-383^(a) 206-231^(b) 627 5′-ATT GTC TAT AAA AAT GGC GAT AAG TC 379-383^(a) 42-67^(b) 626^(c) 5′-TAC CAC CTT TTA AGT AAG GTG CTA AT 379-383^(a) 371-396^(b) 628 5′-AAA ATG GCG ATA AGT CAC AAA AAG TA 379-383^(a) 52-77^(b) 626^(c) 5′-TAC CAC CTT TTA AGT AAG GTG CTA AT 379-383^(a) 371-396^(b) Bacterial group: Campylobacter jejuni and C. coli 2131 5′-AAG CMA TTG TTG TAA ATT TTG AAA G 1576, 1600, 7-31^(e) 1849, 1863, 2139^(d,a) 2132^(c) 5′-TCA TAT CCA TAG CAA TAG TTC TA 1576, 1600, 92-114^(e) 1849, 1863, 2139^(d,a) Bacterial genus: Bordetella sp. 825 5′-ATG AGC ARC GSA ACC ATC GTT CAG TG 1672^(d) 1-26 826^(c) 5′-TCG ATC GTG CCG ACC ATG TAG AAC GC 1672^(d) 1342-1367 Fungal genus: Candida sp. 634 5′-AAC ACY GTC AGR RCI ATT GCY ATG GA 460-472, 101-126^(f) 474-478^(a) 635^(c) 5′-AAA CCR GTI ARR GCR ACT CTI GCT CT 460-472, 617-642^(f) 474-478^(a) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the S. agalactiae atpD sequence fragment (SEQ ID NO. 380). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)Sequence from databases. ^(e)The nucleotide positions refer to the C. jejuni atpD sequence fragment (SEQ ID NO. 1576). ^(f)The nucleotide positions refer to the C. albicans atpD sequence fragment (SEQ ID NO. 460). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Universal primers 562 5′-CAR ATG RAY GAR CCI CCI GGI GYI MGI ATG 243, 244, 262, 528-557^(b) 264, 280, 284, 291, 297, 309, 311, 315, 317, 324, 329, 332, 334-336, 339, 342, 343, 351, 356, 357, 364-366, 370, 375, 379, 393^(a) 563^(c) 5′-GGY TGR TAI CCI ACI GCI GAI GGC AT 243, 244, 262, 687-712^(b) 264, 280, 284, 291, 297, 309, 311, 315, 317, 324, 329, 332, 334-336, 339, 342, 343, 351, 356, 357, 364-366, 370, 375, 379, 393^(a) 564 5′-TAY GGI CAR ATG AAY GAR CCI CCI GGI AA 243, 244, 262, 522-550^(b) 264, 280, 284, 291, 297, 309, 311, 315, 317, 324, 329, 332, 334-336, 339, 342, 343, 351, 356, 357, 364-366, 370, 375, 379, 393^(a) 565^(c) 5′-GGY TGR TAI CCI ACI GCI GAT GGD AT 243, 244, 262, 687-712^(b) 264, 280, 284, 291, 297, 309, 311, 315, 317, 324, 329, 332, 334-336, 339, 342, 343, 351, 356, 357, 364-366, 370, 375, 379, 393^(a) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the K. pneumoniae atpD sequence fragment (SEQ ID NO. 317). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Universal primers (continued) 640 5′-TCC ATG GTI TWY GGI CAR ATG AA 248, 284, 315, 513-535^(b) 317, 343, 357, 366, 370, 379, 393^(a) 641^(c) 5′-TGA TAA CCW ACI GCI GAI GGC ATA CG 248, 284, 315, 684-709^(b) 317, 343, 357, 366, 370, 379, 393^(a) 642 5′-GGC GTI GGI GAR CGI ACI CGT GA 248, 284, 315, 438-460^(b) 317, 343, 357, 366, 370, 379, 393^(a) 641^(c) 5′-TGA TAA CCW ACI GCI GAI GGC ATA CG 248, 284, 315, 684-709^(b) 317, 343, 357, 366, 370, 379, 393^(a) Sequencing primers 566 5′-TTY GGI GGI GCI GGI GTI GGI AAR AC 669^(d) 445-470 567^(c) 5′-TCR TCI GCI GGI ACR TAI AYI GCY TG 669^(d) 883-908 566 5′-TTY GGI GGI GCI GGI GTI GGI AAR AC 669^(d) 445-470 814 5′-GCI GGC ACG TAC ACI GCC TG 666^(d) 901-920 568 5′-RTI ATI GGI GCI GTI RTI GAY GT 669^(d) 25-47 567^(c) 5′-TCR TCI GCI GGI ACR TAI AYI GCY TG 669^(d) 883-908 570 5′-RTI RYI GGI CCI GTI RTI GAY GT 672^(d) 31-53 567^(c) 5′-TCR TCI GCI GGI ACR TAI AYI GCY TG 669^(d) 883-908 572 5′-RTI RTI GGI SCI GTI RTI GA 669^(d) 25-44 567^(c) 5′-TCR TCI GCI GGI ACR TAI AYI GCY TG 669^(d) 883-908 569 5′-RTI RTI GGI SCI GTI RTI GAT AT 671^(d) 31-53 567^(c) 5′-TCR TCI GCI GGI ACR TAI AYI GCY TG 669^(d) 883-908 571 5′-RTI RTI GGI CCI GTI RTI GAT GT 670^(d) 31-53 567^(c) 5′-TCR TCI GCI GGI ACR TAI AYI GCY TG 669^(d) 883-908 ^(a) These sequences were aligned to derive the corresponding primer. ^(b) The nucleotide positions refer to the K. pneumoniae atpD sequence fragment (SEQ ID NO. 317). ^(c) These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d) Sequences from databases. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Sequencing primers (continued) 700 5′-TIR TIG AYG TCG ART TCC CTC ARG 669^(a) 38-61 567^(b) 5′-TCR TCI GCI GGI ACR TAI AYI GCY TG 669^(a) 883-908 568 5′-RTI ATI GGI GCI GTI RTI GAY GT 669^(a) 25-47 573^(b) 5′-CCI CCI ACC ATR TAR AAI GC 666^(a) 1465-1484 574 5′-ATI GCI ATG GAY GGI ACI GAR GG 666^(a) 283-305 573^(b) 5′-CCI CCI ACC ATR TAR AAI GC 666^(a) 1465-1484 574 5′-ATI GCI ATG GAY GGI ACI GAR GG 666^(a) 283-305 708^(b) 5′-TCR TCC ATI CCI ARI ATI GCI ATI AT 666^(a) 1258-1283 681 5′-GGI SSI TTY GGI ISI GGI AAR AC 685 694-716 682^(b) 5′-GTI ACI GGY TCY TCR AAR TTI CCI CC 686 1177-1202 681 5′-GGI SSI TTY GGI ISI GGI AAR AC 685 694-716 683^(b) 5′-GTI ACI GGI TCI SWI AWR TCI CCI CC 685 1180-1205 681 5′-GGI SSI TTY GGI ISI GGI AAR AC 685 694-716 699 5′-GTI ACI GGY TCY TYR ARR TTI CCI CC 686 1177-1202 681 5′-GGI SSI TTY GGI ISI GGI AAR AC 685 694-716 812^(b) 5′-GTI ACI GGI TCY TYR ARR TTI CCI CC 685 1180-1205 1213 5′-AAR GGI GGI ACI GCI GCI ATH CCI GG 714^(a) 697-722 1212^(b) 5′-CCI CCI RGI GGI GAI ACI GCW CC 714^(a) 1189-1211 1203 5′-GGI GAR MGI GGI AAY GAR ATG 709^(a) 724-744 1207^(b) 5′-CCI TCI TCW CCI GGC ATY TC 709^(a) 985-1004 1204 5′-GCI AAY AAC ITC IWM YAT GCC 709^(a) 822-842 1206^(b) 5′-CKI SRI GTI GAR TCI GCC A 709^(a) 926-944 1205 5′-AAY ACI TCI AWY ATG CCI GT 709^(a) 826-845 1207^(b) 5′-CCI TCI TCW CCI GGC ATY TC 709^(a) 985-1004 2282 5′-AGR RGC IMA RAT GTA TGA 714^(a) 84-101 2284^(b) 5′-TCT GWG TRA CIG GYT CKG AGA 714^(a) 1217-1237 2283 5′-ATI TAT GAY GGK ITT CAG AGG C 714^(a) 271-292 2285^(b) 5′-CMC CIC CWG GTG GWG AWA C 714^(a) 1195-1213 ^(a)Sequences from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Annex III: Internal hybridization probes for specific detection of tuf sequences. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial species: Abiotrophia adiacens 2170 5′-ACG TGA CGT TGA CAA ACC A 1715 313-331 Bacterial species: Chlamydia pneumoniae 2089 5′-ATG CTG AAC TTA TTG ACC TT   20 136-155 2090 5′-CGT TAC TGG AGT CGA AAT G  20 467-485 Bacterial species: Enterococcus faecalis 580 5′-GCT AAA CCA GCT ACA ATC ACT CCA C 62-63, 607^(a) 584-608^(b) 603 5′-GGT ATT AAA GAC GAA ACA TC 62-63, 607^(a) 440-459^(b) 1174 5′-GAA CGT GGT GAA GTT CGC 62-63, 607^(a) 398-415^(b) Bacterial species: Enterococcus faecium 602 5′-AAG TTG AAG TTG TTG GTA TT 64, 608^(a) 426-445^(c) Bacterial species: Enterococcus gallinarum 604 5′-GGT GAT GAA GTA GAA ATC GT 66, 609^(a) 419-438^(d) Bacterial species: Escherichia coli 579 5′-GAA GGC CGT GCT GGT GAG AA   78 503-522 2168 5′-CAT CAA AGT TGG TGA AGA AGT TG   78 409-431 Bacterial species: Neisseria gonorrhoeae 2166 5′-GAC AAA CCA TTC CTG CTG  126 322-339^(e) Fungal species: Candida albicans 577 5′-CAT GAT TGA ACC ATC CAC CA 407-411^(a) 406-425^(f) Fungal species: Candida dubliniensis 578 5′-CAT GAT TGA AGC TTC CAC CA 412, 414-415^(a) 418-437^(g) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the E. faecalis tuf sequence fragment (SEQ ID NO. 607). ^(c)The nucleotide positions refer to the E. faecium tuf sequence fragment (SEQ ID NO. 608). ^(d)The nucleotide positions refer to the E. gallinarum tuf sequence fragment (SEQ ID NO. 609). ^(e)The nucleotide positions refer to the N. gonorrhoeae tuf sequence fragment (SEQ ID NO. 126). ^(f)The nucleotide positions refer to the C. albicans tuf(EF-1) sequence fragment (SEQ ID NO. 408). ^(g)The nucleotide positions refer to the C. dubliniensis tuf(EF-1) sequence fragment (SEQ ID NO. 414). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial species: Haemophilus influenzae 581 5′-ACA TCG GTG CAT TAT TAC GTG G 610^(a) 551-572 Bacterial species: Mycoplasma pneumoniae 2095 5′-CGG TCG GGT TGA ACG TGG 2097^(a) 687-704 Bacterial species: Staphylococcus aureus 584 5′-ACA TGA CAC ATC TAA AAC AA 176-180^(b) 369-388^(c) 585 5′-ACC ACA TAC TGA ATT CAA AG 176-180^(b) 525-544^(c) 586 5′-CAG AAG TAT ACG TAT TAT CA 176-180^(b) 545-564^(c) 587 5′-CGT ATT ATC AAA AGA CGA AG 176-180^(b) 555-574^(c) 588 5′-TCT TCT CAA ACT ATC GTC CA 176-180^(b) 593-612^(c) Bacterial species: Staphylococcus epidermidis 589 5′-GCA CGA AAC TTC TAA AAC AA 185, 611^(b) 445-464^(d) 590 5′-TAT ACG TAT TAT CTA AAG AT 185, 611^(b) 627-646^(d) 591 5′-TCC TGG TTC TAT TAC ACC AC 185, 611^(b) 586-605^(d) 592 5′-CAA AGC TGA AGT ATA CGT AT 185, 611^(b) 616-635^(d) 593 5′-TTC ACT AAC TAT CGC CCA CA 185, 611^(b) 671-690^(d) Bacterial species: Staphylococcus haemolyticus 594 5′-ATT GGT ATC CAT GAC ACT TC 186, 188-190^(b) 437-456^(e) 595 5′-TTA AAG CAG ACG TAT ACG TT 186, 188-190^(b) 615-634^(e) Bacterial species: Staphylococcus hominis 596 5′-GAA ATT ATT GGT ATC AAA GA 191, 193-196^(b) 431-450^(f) 597 5′-ATT GGT ATC AAA GAA ACT TC 191, 193-196^(b) 437-456^(f) 598 5′-AAT TAC ACC TCA CAC AAA AT 191, 193-196^(b) 595-614^(f) ^(a)Sequences from databases. ^(b)These sequences were aligned to derive the corresponding probe. ^(c)The nucleotide positions refer to the S. aureus tuf sequence fragment (SEQ ID NO. 179). ^(d)The nucleotide positions refer to the S. epidermidis tuf sequence fragment (SEQ ID NO. 611). ^(e)The nucleotide positions refer to the S. haemolyticus tuf sequence fragment (SEQ ID NO. 186). ^(f)The nucleotide positions refer to the S. hominis tuf sequence fragment (SEQ ID NO. 191). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial species: Staphylococcus saprophyticus 599 5′-CGG TGA AGA AAT CGA AAT CA 198-200^(a) 406-425^(b) 600 5′-ATG CAA GAA GAA TCA AGC AA 198-200^(a) 431-450^(b) 601 5′-GTT TCA CGT GAT GAT GTA CA 198-200^(a) 536-555^(b) 695 5′-GTT TCA CGT GAT GAC GTA CA 198-200^(a) 563-582^(b) Bacterial species: Streptococcus agalactiae 582^(c) 5′-TTT CAA CTT CGT CGT TGA CAC GAA CAG T 207-210^(a) 404-431^(d) 583^(c) 5′-CAA CTG CTT TTT GGA TAT CTT CTT TAA TAC CAA CG 207-210^(a) 433-467^(d) 1199 5′-GTA TTA AAG AAG ATA TCC AAA AAG C 207-210^(a) 438-462^(d) Bacterial species: Streptococcus pneumoniae 1201 5′-TCA AAG AAG AAA CTA AAA AAG CTG T 971, 977, 513-537^(e) 979, 986^(a) Bacterial species: Streptococcus pyogenes 1200 5′-TCA AAG AAG AAA CTA AAA AAG CTG T 1002 473-497 Bacterial group: Enterococcus casseliflavus-flavescens- gallinarum group 620 5′-ATT GGT GCA TTG CTA CGT 58, 65, 66^(a) 527-544^(f) 1122 5′-TGG TGC ATT GCT ACG TGG 58, 65, 66^(a) 529-546^(f) Bacterial group: Enterococcus sp., Gemella sp., A. adiacens 2172 5′-GTG TTG AAA TGT TCC GTA AA 58-62, 67-71, 477-496^(g) 87-88, 607-609, 727, 871 1715, 1722^(a) ^(a)These sequences were aligned to derive the corresponding primer. ^(b) The nucleotide positions refer to the S. saprophyticus tuf sequence fragment (SEQ ID NO. 198). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)The nucleotide positions refer to the S. agalactiae tuf sequence fragment (SEQ ID NO. 209). ^(e)The nucleotide positions refer to the S. pneumoniae tuf sequence fragment (SEQ ID NO. 986). ^(f)The nucleotide positions refer to the E. flavescens tuf sequence fragment (SEQ ID NO. 65). ^(g)The nucleotide positions refer to the E. faecium tuf sequence fragment (SEQ ID NO. 608). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial genus: Gemella 2171 5′-TCG TTG GAT TAA CTG AAG AA 87, 88^(a) 430-449^(b) Bacterial genus: Staphylococcus sp. 605 5′-GAA ATG TTC CGT AAA TTA TT 176-203^(a) 403-422^(c) 606 5′-ATT AGA CTA CGC TGA AGC TG 176-203^(a) 420-439^(c) 1175 5′-GTT ACT GGT GTA GAA ATG TTC 176-203^(a) 391-411^(c) 1176 5′-TAC TGG TGT AGA AAT GTT C 176-203^(a) 393-411^(c) Bacterial genus: Streptococcus sp. 1202 5′-GTG TTG AAA TGT TCC GTA AAC A 206-231, 971, 466-487^(d) 977, 979, 982-986^(a) Fungal species: Candida albicans 1156 5′-GTT GAA ATG CAT CAC GAA CAA TT 407-412, 624^(a) 680-702^(e) Fungal group: Candida albicans and C. tropicalis 1160 5′-CGT TTC TGT TAA AGA AAT TAG AAG 407-412, 748-771^(e) 429, 624^(a) Fungal species: Candida dubliniensis 1166 5′-ACG TTA AGA ATG TTT CTG TCA A 414-415^(a) 750-771^(f) 1168 5′-GAA CAA TTG GTT GAA GGT GT 414-415^(a) 707-726^(f) Fungal species: Candida glabrata 1158 5′-AAG AGG TAA TGT CTG TGG T  417 781-799 1159 5′-TGA AGG TTT GCC AGG TGA  417 718-735 Fungal species: Candida krusei 1161 5′-TCC AGG TGA TAA CGT TGG  422 720-737 ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the G. haemolysans tuf sequence fragment (SEQ ID NO. 87). ^(c)The nucleotide positions refer to the S. aureus tuf sequence fragment (SEQ ID NO. 179). ^(d)The nucleotide positions refer to the S. pneumoniae tuf sequence fragment (SEQ ID NO. 986). ^(e)The nucleotide positions refer to the C. albicans tuf(EF-1) sequence fragment (SEQ ID NO. 408). ^(f)The nucleotide positions refer to the C. dubliniensis tuf(EF-1) sequence fragment (SEQ ID NO. 414). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Fungal group: Candida lusitaniae and C. guillermondii 1162 5′-CAA GTC CGT GGA AAT GCA 418, 424^(a) 682-699^(b) Fungal species: Candida parapsilosis 1157 5′-AAG AAC GTT TCA GTT AAG GAA AT  426 749-771 Fungal species: Candida zeylanoides 1165 5′-GGT TTC AAC GTG AAG AAC  432 713-730 Fungal genus: Candida sp. 1163 5′-GTT GGT TTC AAC GTT AAG AAC 407-412, 414-415, 728-748^(c) 417, 418, 422, 429^(a) 1164 5′-GGT TTC AAC GTC AAG AAC 413, 416, 420, 740-757^(b) 421, 424, 425, 426, 428, 431^(a) 1167 5′-GTT GGT TTC AAC GT 406-426, 428-432, 728-741^(c) 624^(a) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the C. lusitaniae tuf(EF-1) sequence fragment (SEQ ID NO. 424). ^(c)The nucleotide positions refer to the C. albicans tuf(EF-1) sequence fragment (SEQ ID NO. 408).

Annex IV: Strategy for the selection of amplification/sequencing primers from atpD (F-type) sequences. SEQ ID 23                         49   443                           472   881                             910 NO.: Accession #: B. cepacia AGTgCAT CGGCGCCGTT ATCGACGTGG...TGTTCG GCGGTGCTGG CGTGGGC AAG ACCG...TCCA GGCCGTGT ACGTCCCTGC GGACGACT — X76877 B. pertussis AGTgCAT CGGCGCCGTG GTGGATATTC...TGTTCG GCGGCGCCGG CGTGGGC AAG ACCG...TCCA GGCCGTGT ACGTGCCTGC CGACGACT — Genome project P. aeruginosa AAATCAT CGGCGCCGTG ATCGACGTGG...TGTTCG GCGGCGCCGG CGTGGGC AAG ACCG...TCCA GGCCGTAT ACGTTCCCGC GGACGACC — Genome project E. coli AGGTAAT CGGCGCCGTA GTTGACGTCG...TGTTCG GTGGTGCGGG TGTAGGT AAA ACCG...TACA GGCAGTAT ACGTACCTGC GGATGACT — J01594 N. gonorrhoeae AAATTAT CGGTGCGGTT GTTGACGTGG...TGTTCG GCGGTGCCGG TGTGGGT AAA ACCG...TCCA AGCCGTAT ATGTACCTGC GGATGACT — Genome project M. thermoacetica AGGTTAT TGGCCCGGTG GTTGACGTCG...TCTTCG GCGGCGCCGG GGTCGGC AAG ACGG...TGCA AGCTATCT ATGTGCCGGC CGACGACC — U64318 S. aurantiaca AGGTTcT CGGTCCCGTG ATTGACGTGG...TGTTCG GCGGCGCCGG CGTGGGC AAG ACGG...TGCA GGCCATCT ACGTGCCCGC CGACGACC — X76879 M. tuberculosis GGGTCAC TGGGCCCGTC GTCGACGTCG...TGTTCG GCGGTGCCGG GGTGGGC AAG ACGG...TGCA AGCCGTCT ACGTGCCCGC CGACGACT — Z73419 B. fragilis AGGTAAT TGGCCCTGTG GTCGATGTGT...TGTTTG GCGGGGCCGG AGTGGGT AAA ACTG...TGCA GGCTGTTT ACGTACCGGC TGATGACT — M22247 C. lytica AAATTAT TGGCCCAGTT ATAGATGTGG...TATTTG GAGGTGCCGG AGTAGGT AAA ACAG...TACA GGCGGTTT ACGTACCTGC GGATGATT 672 M22535 A. woodii AGGTTAT TGGACCAGTA GTCGATGTTA...TTTTCG GTGGTGCCGG AGTTGGT AAA ACCG...TTCA GGCCGTTT ACGaTCCAGC CGATGACT — U10505 C. acetobutylicum AGGTAAT AGGACCTGTT GTGGATATTA...TGTTCG GTGGTGCCGG TGTTGGT AAA ACAG...TTCA GGCTGTAT ATGTTCCTGC TGATGACC 671 AF101055 M. pneumoniae AAGTGAT TGGCCCGGTA GTTGATGTCA...TATTTG GTGGTGCTGG TGTTGGT AAA ACGG...TGCA AGCGATCT ATGTGCCAGC TGATGACT — U43738 H. pylori AGGTTtT AGGCCCGGTG GTAGATGTGG...TGTTTG GTGGGGCTGG CGTAGGC AAA ACGG...TTCA AGCGGTGT ATGTGCCAGC AGACGACT 670 AF004014 Selected sequences   RTIAT IGGIGCIGTI RTIGAYGT 568 for universal primers   RTIRY IGGICCIGTI RTIGAYGT 570   RTIRT IGGISCIGTI RTIGA 572   RTIRT IGGISCIGTI RTIGATAT 569   RTIRT IGGICCIGTI RTIGATGT 571                                   TTYG GIGGIGCIGG IGTIGGIAAR AC 566 Selected sequence                                                                       CA RGCIRTIT AYGTICCIGC IGAYGA 567 for universal primer^(a) The sequence numbering refers to the Escherichia coli atpD gene fragment (SEQ ID NO. 669). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)This sequence is the reverse-complement of the selected primer.

Annex V: Strategy for the selection of universal amplification/sequencing primers from atpD (V-type) sequences. SEQ 691                          719   1177                           1208 ID NO.: E. hirae CC AGGTCCGTTT GGTGCAGGGA AGACAGT...TCTGGTGGAg ATaTCtctGA ACCAGTGACT CA 685 H. salinarum CC GGGGCCGTTC GGGTCCGGGA AGACGGT...CCCGGCGGGg ACTTCtccGA GCCGGTCACC CA 687 T. thermophilus CC TGGGCCCTTC GGCAGCGGCA AGACCGT...CCGGGCGGCg ACaTgtccGA GCCCGTGACC CA 693 Human CC TGGGGCCTTC GGATGTGGCA AGACTGT...CCCGGTGGAg ACTTCtcAGA tCCCGTGACG AC 688 T. congolense CC TGGCGCGTTT GGATGCGGAA AGACGGT...CCTGGAGGTg ACTTTtctGA cCCAGTGACG TC 692 P. falciparum CC TGGTGCATTT GGTTGTGGAA AAACTTG...CCAGGTGGTg ATTTCtctGA cCCTGTAACT AC 689 C. pneumoniae CC AGGACCTTTT GGTGCAGGGA AAACAGT...GCAGGAGGAA ACTTTGAAGA ACCAGTCACT CA 686 Selected sequences     GGISSITTY GGIISIGGIA ARAC 681 for universal primers Selected sequences                                       GGIGGIA AYTTYGARGA RCCIGTIAC 682 for universal primers^(a)                                       GGIGGIG AYWTIWSIGA ICCIGTIAC 683 The sequence numbering refers to the Enterococcus hirae atpD gene fragment (SEQ ID NO. 685). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches for SEQ ID NOs. 681 and 682 are indicated by lower-case letters. Mismatches for SEQ ID NO. 683 are indicated by underlined nucleotides. Dots indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)These sequences are the reverse-complement of the selected primers.

Annex VI: Strategy for the selection of universal amplification/sequencing primers from tuf (M) sequences (organelle origin). 601                                635 C. neoformans ^(a) AAGAA CATGATCACC GGTaCCtCCC AGgctGACTG... S. cerevisiae ^(a) AAGAA CATGATTACT GGTaCTtCTC AAgctGACTG... O. volvulus ^(a) AAGAA TATGATCACA GGTaCTtCTC AGgctGACTG... Human^(a) AAAAA CATGATTACA GGGaCAtCTC AGgctGACTG... G. maxB1^(b) AAGAA CATGATCACC GGCGCTGCCC AGATGGACGG... G. maxB2^(b) AAAAA CATGATCACC GGCGCCGCCC AGATGGACGG... E. coli ^(c) AAAAA CATGATCACC GGTGCTGCTC AGATGGACGG... S. aureofaciens ^(c) AAGAA CATGATCACC GGTGCCGCCC AGATGGACGG... E. tenella ^(b) AAAAA TATGATTACA GGAGCAGCAC AAATGGATGG... T. gondii ^(b) AAGAA TATGATTACT GGAGCCGCAC AAATGGATGG... S. cerevisiae ^(b) AAGAA TATGATTACC GGTGCTGCTC AAATGGATGG... A. thaliana ^(b) AAAAA TATGATTACT GGAGCTGCGC AAATGGATGG... Selected sequence for    AA YATGATIACI GGIGCIGCIC ARATGGA universal primer Selected sequences                                            for universal primers                                            SEQ ID Accession 1479                            1511 NO.: #: C. neoformans ^(a) CGCcgTCcGA GAcatGcGAC AGACcGTTGc CGT — U81803 S. cerevisiae ^(a) CGCTgTCAGA GAcatGaGAC AAACTGTcGc TGT 665 X00779 O. volvulus ^(a) TGCTgTGcGt GAtatGaGAC AAACaGTTGc GGT — M64333 Human^(a) TGCTgTTcGt GAtatGaGAC AGACaGTTGc TGT — X03558 G. maxB1^(b) TGCTATTAGA GAAGGAGGCA AAACTGTTGG AGC — Y15107 G. maxB2^(b) TGCTATTAGA GAAGGAGGCA AAACTGTTGG AGC — Y15108 E. coli ^(c) CGCaATCcGt GAAGGGGCC GTACcGTTGG CGC  78 — S. aureofaciens ^(c) CGCcATCcGt GAGGGTGGTC GTACcGTgGG CGC — AF007125 E. tenella ^(b) TGCTATAAGAGAAGGAGGAA AAACTATAGG AGC — AI755521 T. gondii ^(b) TGCTATTAGA GAAGGAGGTC GTACTATAGG AGC — Y11431 S. cerevisiae ^(b) CAATATCAGA GAGGGTGGAA GAACTGTTGG TAC 619 K00428 A. thaliana ^(b) TGCctTAAGG GAAGGAGGTA GAACaGTTGG AGC — X89227 Selected 664 sequence for universal primer Selected     TATIAGR GARGGIGGIM RIACTRTWGG ^(d) 652 sequences    ATCCGT GAGGGYGGCC GITCIGT ^(d) 561 for universal primers The sequence numbering refers to the Saccharomyces cerevisiae tuf (M) gene (SEQ ID NO. 619). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches for SEQ ID NOs. 652 and 664 are indicated by lower-case letters. Mismatches for SEQ ID NO. 561 are indicated by underlined nucleotides. Dots indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)This sequence refers to tuf(EF-1) gene. ^(b)This sequence refers to tuf (M) or organelle gene. ^(c)This sequence refers to tuf gene from bacteria. ^(d)These sequences are the reverse-complement of the selected primers.

Annex VII: Strategy for the selection of eukaryotic sequencing primers from tuf (EF-1) sequences. SEQ ID Accession 154                       179   286                          314 NO.: #: S. cerevisiae GG TTCTTTCAAG TACGCTTGGG TTTT...AGAGA TTTCATCAAG AACATGATTA CTGG... 665 X00779 B. hominis GG CTCCTTCAAG TACGCGTGGG TGCT...CGTGA CTTCATaAAG AACATGATCA CGGG... — D64080 C. albicans GG TTCTTTCAAA TACGCTTGGG TCTT...AGAGA TTTCATCAAG AATATGATCA CTGG... — M29934 C. neoformans TC TTCTTTCAAG TACGCTTGGG TTCT...CGAGA CTTCATCAAG AACATGATCA CCGG... — U81803 E. histolytica GG ATCATTCAAA TATGCTTGGG TCTT...AGAGA TTTCATTAAG AACATGATTA CTGG... — M92073 G. lamblia GG CTCCTTCAAG TACGCGTGGG TCCT...CGCGA CTTCATCAAG AACATGATCA CGGG... — D14342 H. capsulatum AA ATCCTTCAAA TATGCGTGGG TCCT...CGTGA CTTCATCAAG AACATGATCA CTGG... — U14100 Human GG CTCCTTCAAG TATGCCTGGG TCTT...AGAGA CTTtATCAAA AACATGATTA CAGG... — X03558 L. braziliensis GC GTCCTTCAAG TACGCGTGGG TGCT...CGCGA CTTCATCAAG AACATGATCA CCGG... — U72244 O. volvulus GG CTCATTTAAA TATGCTTGGG TATT...CGTGA TTTCATTAAG AATATGATCA CAGG... — M64333 P. berghei GG TagTTTCAAA TATGCATGGG TTTT...AAAc A TTTtATTAAA AATATGATTA CTGG... — AJ224150 P. knowlesi GG AagTTTTAAG TACGCATGGG TGTT...AAGGA TTTCATTAAA AATATGATTA CCGG... — AJ224153 S. pombe GG TTCCTTCAAG TACGCCTGGG TTTT...CGTGA TTTCATCAAG AACATGATTA CCGG... — U42189 T. cruzi TC TTCTTTCAAG TACGCGTGGG TCTT...CGCGA CTTCATCAAG AACATGATCA CGGG... — L76077 Y. lipolytica GG TTCTTTCAAG TACGCTTGGG TTCT...CGAGA TTTCATCAAG AACATGATCA CCGG... — AF054510 Selected sequences for     TCITTYAAR TAYGCITGGG T 558 amplification primers                                    GA YTTCATYAAR AAYATGATYA C 560                                    GA YTTCATIAAR AAYATGAT 653 The sequence numbering refers to the Saccharomyces cerevisiae tuf (EF-1) gene fragment (SEQ ID NO. 665). Nucleotides in capitals are identical to the selected sequences SEQ ID NOs. 558, 560 or 653, or match those sequences. Mismatches for SEQ ID no. 558 and 560 are indicated by lower-case letters. Mismatches for SEQ ID NO. 653 are indicated by underlined nucleotides. Dots indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C. or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. SEQ ID Accession    751                      776   1276                        1304 NO.: #: S. cerevisiae ...GTTTACAA GATCGGTGGT ATTGGTAC...GACATG AGACAAACTG TCGCTGTCGG TGT 665 X00779 B. hominis ...GTGTACAA GATTGGCGGT ATTGGTAC...GATATG AGACAGACTG TCGCTGTCGG TAT — D64080 C. albicans ...GTTTACAA GATCGGTGGT ATTGGTAC...GATATG AGACAAACCG TTGCTGTtGG TGT — M29934 C. neoformans ...GTCTACAA GATCGGTGGT ATCGGCAC...GACATG CGACAGACCG TTGCCGTtGG TGT — U81803 E. histolytica ...GTTTACAA GATTTcAGGT ATTGGAAC...GATATG AaACAAACCG TTGCTGTtGG AGT — M92073 G. lamblia ...GTCTACAA GATCTcGGGc gTCGGGAC...~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~~ — D14342 H. capsulatum ...GTGTACAA AATCTcTGGT ATTGGCAC...GACATG AGACAAACCG TCGCTGTCGG TGT — U14100 Human ...GTCTACAA AATTGGTGGT ATTGGTAC...GATATG AGACAGACAG TTGCgGTgGG TGT — X03558 L. braziliensis ...GTGTACAA GATCGGCGGT ATCGGCAC...GACATG CGCagAACGG TCGCCGTCGG CAT — U72244 O. volvulus ...GTTTACAA AATTGGAGGT ATTGGAAC...GATATG AGACAAACAG TTGCTGTtGG CGT — M64333 P. berghei ...GTATACAA AATTGGTGGT ATTGGTAC...GATATG AGACAAACAA TTGCTGTCGG TAT — AJ224150 P. knowlesi ...GTATACAA AATCGGTGGT ATTGGTAC...GATATG AGACAAACCA TTGCTGTCGG TAT — AJ224153 S. pombe ...GTTTACAA GATCGGTGGT ATTGGTAC...GACATG CGTCAAACCG TCGCTGTCGG TGT — U42189 T. cruzi ...GTGTACAA GATCGGCGGT ATCGGCAC...GAC ATG CGCCAGACGG TCGCCGTCGG CAT — L76077 Y. lipolytica ...GTCTACAA GATCGGTGGT ATCGGCAC...GACATG CGACAGACCG TTGCTGTCGG TGT — AF054510 Selected sequence for       TACAA RATYKGIGGT ATYGG 654 amplification primer Selected sequences for       TACAA RATYKGIGGT ATYGG 655 amplification primers^(a)                                      ATG MGICARACIR TYGCYGTCGG 559 The sequence numbering refers to the Saccharomyces cerevisiae tuf (EF-1) gene fragment (SEQ ID NO. 665). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. “~” indicate incomplete sequence data. Dots indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)This sequences are the reverse-complement of the selected primers.

Annex VIII: Strategy for the selection of Streptococcus agalactiae-specific amplification primers from tuf sequences. SEQ Accession 305                           334   517                       542 ID NO.: #: S. agalactiae CCAGAA CGTGATACTG ACAAACCTTT ACTT...GGAC AACGTTGGTG TTCTTCTTCG TG 207 — S. agalactiae CCAGAA CGTGATACTG ACAAACCTTT ACTT...GGAC AACGTTGGTG TTCTTCTTCG TG 208 — S. agalactiae CCAGAA CGTGATACTG ACAAACCTTT ACTT...GGAC AACGTTGGTG TTCTTCTTCG TG 209 — S. agalactiae CCAGAA CGTGATACTG ACAAACCTTT ACTT...GGAC AACGTTGGTG TTCTTCTTCG TG 210 — S. anginosus CCAGAA CGTGAcACTG ACAAACCaTT gCTT...AGAt AACGTaGGgG TTCTTCTTCG TG 211 — S. anginosus CCAGAA CGTGATACTG ACAAACCaTT gCTT...AGAt AACGTaGGTG TTCTTCTTCG TG 221 — S. bovis CCAaAA CGTGATACTG ACAAACCaTT gCTT...GGAt AACGTTGGTG TTCTTCTTCG TG 212 — S. gordonii CCAGAA CGTGAcACTG ACAAACCaTT gCTT...AGAt AAtGTaGGTG TcCTTCTTCG TG 223 — S. mutans CCAGAA CGTGATACTG ACAAgCCgcT cCTT...GGAt AAtGTTGGTG TTCTcCTTCG TG 224 — S. pneumoniae CCAGAA CGTGAcACTG ACAAACCaTT gCTT...AGAt AACGTaGGTG TcCTTCTTCG TG 145^(a) S. sanguinis CCAGAA CGcGATACTG ACAAgCCaTT gCTT...GGAC AACGTaGGTG TgCTTCTcCG TG 227 — S. sobrinus CCAaAA CGcGATACTG AtAAgCCaTT gCTT...AGAt AACGTTGGTG TgCTTCTTCG TG 228 — B. cepacia CCGGAg CGTGcagtTG ACggcgCgTT cCTG...CGAC AACGTTGGTa TcCTgCTgCG cG  16 — B. fragilis CCTccg CGcGATgtTG AtAAACCTTT ctTG...TGAC AACGTaGGTc TgtTgCTTCG TG — P33165 B. subtilis CCAGAA CGcGAcACTG AaAAACCaTT caTG...TGAC AACaTTGGTG ccCTTCTTCG cG — Z99104 C. diphtheriae CCAGAg CGTGAgACcG ACAAgCCaTT cCTC...CGAC AACtgTGGTc TgCTTCTcCG TG 662 — C. trachomatis CCAGAA aGaGAaAtTG ACAAgCCTTT cTTA...AGAg AAtGTTGGat TgCTcCTcaG aG  22 — E. coli CCAGAg CGTGcgAtTG ACAAgCCgTT cCTg...TGAg AACGTaGGTG TTCTgCTgCG TG  78 — G. vaginalis CCAact CacGATctTG ACAAgCCaTT cTTg...CGAt RACacTGGTc TTCTTCTcCG cG 135^(a) S. aureus CCAGAA CGTGATtCTG ACAAACCaTT cATg...TGAC AACaTTGGTG catTatTaCG TG 179 — Selected sequence for    GAA CGTGATACTG ACAAACCTTT A 549 species-specific primer Selected sequence for                                        C AACGTTGGTG TTCTTCTTC 550 species-specific primer^(b) The sequence numbering refers to the Streptococcus agalactiae tuf gene fragment (SEQ ID NO. 209). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)The SEQ ID NO. refers to previous patent publication WO98/20157. ^(b)This sequence is the reverse-complement of the selected primer.

Annex IX: Strategy for the selection of Streptococcus agalactiae-specific hybridization probes from tuf sequences. SEQ ID Accession 401                            431 433                                    470 NO.: #: S. GGTACTGT TaaaGTtAAt GACGAAGTTG AAATCGTTGG TATcAAAGAc GAaATCtctA AAGCAGTTGT TA 206 acidominimus S. agalactiae GGTACTGT TCGTGTCAAC GACGAAGTTG AAATCGTTGG TATTAAAGAA GATATCCAAA AAGCAGTTGT TA 209 S. agalactiae GGTACTGT TCGTGTCAAC GACGAAGTTG AAATCGTTGG TATTAAAGAA GATATCCAAA AAGCAGTTGT TA 144^(a) S. agalactiae GGTACTGT TCGTGTCAAC GACGAAGTTG AAATCGTTGG TATTAAAGAA GATATCCAAA AAGCAGTTGT TA 207 S. agalactiae GGTACTGT TCGTGTCAAC GACGAAGTTG AAATCGTTGG TATTAAAGAA GATATCCAAA AAGCAGTTGT TA 210 S. agalactiae GGTACTGT TCGTGTCAAC GACGAAGTTG AAATCGTTGG TATTAAAGAA GATATCCAAA AAGCAGTTGT TA 208 S. anginosus GGTACTGT TaaaGTCAAC GACGAAGTTG AAATCGTTGG TATccgtGAt GAaATCCAAA AAGCAGTTGT TA 211 S. anginosus GGTACTGT TaaaGTCAAC GAtGAAGTTG AAATCGTTGG TATccgcGAg GAaATCCAAA AAGCAGTTGT TA 221 S. bovis GGTACTGT TaaaGTCAAC GACGAAGTTG AAATCGTTGG TATccgtGAc GAcATCCAAA AAGCtGTTGT TA 212 S. anginosus GGTACTGT TaaaGTCAAt GAtGAAGTTG AAATCGTTGG TATTcgtGAc GAaATCCAAA AAGCAGTTGT TA 213 S. cricetus GGTACTGT TaagGTCAAt GACGAAGTTG AAATCGTTGG TATcAAgGAc GAaATCCAAA AAGCgGTTGT TA 214 S. cristatus GGTACTGT TCGTGTCAAC GAtGAAaTcG AAATCGTTGG TATcAAAGAA GAaATCCAAA AAGCAGTTGT TA 215 S. downei GGTACTGT TaagGTCAAC GACGAAGTTG AAATCGTTGG TATcAAgGAc GAaATCCAAA AAGCAGTTGT TA 216 S. GGTACTGT TCGTGTCAAC GACGAAaTcG AAATCGTTGG TATcAAAGAA GAaActaAAA AAGCtGTTGT TA 217 dysgalactiae S. equi equi GGTACTGT TCGTGTCAAC GACGAAaTcG AAATCGTTGG TATcAgAGAc G AgATCaAAA AAGCAGTTGT TA 218 S. ferus GGTACTGT aaGaGTCAAC GAtGAAGTTG AAATCGTTGG TATcAAAGAc GAaATCactA AAGCAGTTGT TA 219 S. gordonii GGTAtcGT TaaaGTCAAt GACGAAaTcG AAATCGTTGG TATcAAAGAA GAaATCCAAA AAGCAGTTGT TA 220 S. macacae GGTACTGT TaagGTtAAt GAtGAAGTTG AAATCGTTGG TATTcgtGAc GATATtCAAA AAGCAGTTGT TA 222 S. gordonii GGTAtcGT TaaaGTCAAC GACGAAaTcG AAATCGTTGG TATcAAAGAA GAaActCAAA AAGCAGTTGT TA 223 S. mutans GGTACTGT TaaaGTtAAC GAtGAAGTTG AAATCGTTGG TATccgtGAt GAcATtCAAA AAGCtGTTGT TA 224 S. oralis GGTACTGT TCGTGTCAAC GACGAAaTcG AAATCGTTGG TATcAAAGAA GAaActCAAA AAGCAGTTGT TA — P33170 S. GGTgtTGT TCGTGTCAAt GAtGAAaTcG AAATCGTTGG TATcAAAGAA GAaATCCAAA AAGCAGTTGT TA 225 parasanguinis S. pneumoniae GGTAtcGT TaaaGTCAAC GACGAAaTcG AAATCGTTGG TATcAAAGAA GAaActCAAA AAGCAGTTGT TA 145^(a) S. pyogenes GGTACTGT TCGTGTCAAC GACGAAaTcG AAATCGTTGG TATcAAAGAA GAaActaAAA AAGCtGTTGT TA — Genome project S. ratti GGTACTGT TaaaGTCAAt GACGAAGTTG AAATCGTTGG TATccgtGAt GAcATCCAAA AAGCtGTTGT TA 226 S. salivarius GGTgtTGT TCGTGTCAAt GACGAAGTTG AAATCGTTGG TcTTAAAGAA GAcATCCAAA AAGCAGTTGT TA 146^(a) S. sanguinis GGTAtcGT TaaaGTCAAC GACGAAaTcG AAATCGTTGG TATcAAAGAA GAaATCCAAA AAGCAGTTGT TA 227 S. sobrinus GGTACTGT TaagGTCAAC GACGAAGTTG AAATCGTTGG TATccgtGAc GATATCCAAA AAGCAGTTGT TA 228 S. suis GGTACTGT TCGTGTCAAC GACGAAaTcG AAATCGTTGG TcTTcAAGAA GAaAaatcta AAGCAGTTGT TA 229 S. uberis GGTACTGT TCGTGTCAAC GACGAAaTTG AAATCGTTGG TATcAAAGAA GAaActaAAA AAGCAGTTGT TA 230 S. GGTgtTGT TCGTGTtAAt GACGAAGTTG AAATCGTTGG TcTTAAAGAA GAaATCCAAA AAGCAGTTGT TA 231 vestibularis Selected sequences for    ACTGT TCGTGTCAAC GACGAAGTTG AAA 582 species-specific hybridization                                    CGTTGG TATTAAAGAA GATATCCAAA AAAGTTG 583 probes^(b) The sequence numbering refers to the Streptococcus agalactiae tuf gene fragment (SEQ ID NO. 209). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. ^(a)The SEQ ID NO. refers to previous patent publication WO98/20157. ^(b)These sequences are the reverse-complement of the selected probes.

Annex X: Strategy for the selection of Streptococcus agalactiae-specific amplification primers from atpD sequences. SEQ ID 39                                         80   203                             234   368                             399 NO.: S. agalactiae TT GATTGTCTAT AAAAATGGCG ATAAGTCACA AAAAGTAGTA...TAAGGATA CTTTGGGTCG TGTCTTCAAC GTTC...CTT ATTAGCACCT TACTTAAAAG GTGGTAAAG 380 S. agalactiae TT GATTGTCTAT AAAAATGGCG ATAAGTCACA AAAAGTAGTA...TAAGGATA CTTTGGGTCG TGTCTTCAAC GTTC...CTT ATTAGCACCT TACTTAAAAG GTGGTAAAG 379 S. agalactiae TT GATTGTCTAT AAAAATGGCG ATAAGTCACA AAAAGTAGTA...TAAGGATA CTTTGGGTCG TGTCTTCAAC GTTC...CTT ATTAGCACCT TACTTAAAAG GTGGTAAAG 381 S. agalactiae TT GATTGTCTAT AAAAATGGCG ATAAGTCACA AAAAGTAGTA...TAAGGATA CTTTGGGTCG TGTCTTCAAC GTTC...CTT ATTAGCACCT TACTTAAAAG GTGGTAAAG 382 S. agalactiae TT GATTGTCTAT AAAAATGGCG ATAAGTCACA AAAAGTAGTA...TAAGGATA CTTTGGGTCG TGTCTTCAAC GTTC...CTT ATTAGCACCT TACTTAAAAG GTGGTAAAG 383 S. bovis TT GATTGTtTAT AAAgATGGCG ATAAGTCtCA AAAAaTcGTg...TAAaGAaA CTTTGGGTCG TGTgTTtAAt GTTC...CcT tcTtGCcCCT TACcTAAAAG GTGGTAAAG —^(a) S. salivarius TT GgTcGTtTAT ActgATGaac AaAAGTCtaA AcgtaTcGTg...TAAaGATA CccTtGGaCG TGTCTTtAAC GTTC...CTT gcTAGCcCCT TACcTtAAgG GTGGTAAAG 387 S. pneumoniae cT tgTcGTCTAc AAAAATGaCG AaAgaaaAac AAAAaTcGTc...TAAaGAaA CTTTGGGaCG TGTCTTCAAC GTTt...CcT tcTtGCcCCT TACcTtAAAG GTGGTAAAG —^(b) S. pyogenes TT GATTGTtTAT AAAgATaGtG ATAAaaagCA AAAAaTcGTc...TAAaGAaA CTTTGGGaCG cGTCTTtAAt GTaC...CcT tcTtGCcCCT TACcTtAAAG GTGGTAAAG —^(c) S. anginosus cT tgTaGTCTAT AAAAATGaCG AaAAtaaAtc AAAAaTcGTc...gAAaGAaA CacTtGGTCG cGTCTTtAAC GTTt...CcT tTTAGCcCCc TACcTcAAAG GTGGgAAAG 386 S. sanguinis cT tgTaGTCTAT AAAAATGatG AgAAaaaAtc AAAAaTcGTc...aAAGGAaA CTcTaGGcCG gGT gTTCAAt GTTt...CcT gcTAGCACCT TAtcTgAAAG GTGGgAAAG —^(d) S. mutans TT GgTcGTtTAT AAAgATGGCG AcAAGTCtCA AAgAaTtGTt...aAAaGAaA CacTaGGTCG TGTCTTtAAt GTTC...CcT tcTtGCcCCT TAtcTtAAAG GTGGTAAAG —^(e) B. anthracis gT aAaacagagc AAcgAaaaCG gaAcaagcat tAActTAacA...TgAtGcaA CacTtGGTCG TGTaTTtAAC GTat...CTT AcTtGCtCCT TACaTtAAgG GTGGTAAga 247 B. cereus gT aAaacaaagc AAcgAaaaCG g...aagcat gAActTAacA...TgAtGcaA CacTtGGaCG TGTaTTCAAC GTat...CTT AcTtGCtCCT TACaTtAAgG GTGGTAAga 248 E. faecium TT agTTGTtTAT AAAAATGaCG AaAAtaaAtc AAAAGTtGTt...TAAaGAaA CaTTaGGTCG cGTaTTCAAC GTaC...tTT gcTtGCcCCa TAtTTAAAAG GTGGgAAAG 292 E. gallinarum TT GATcGTtTAc AAAAAaGaCG AgAAaaaAac AAAAGTAGTA...aAcaGATA CTcTaGGcCG aGTaTTtAAt GTaC...tTT ATTAGCtCCT TACTTAAAAG GTGGTAAAG 293 E. faecalis TT agTcGTtTAT AAAAATGGCG AagcaaaACA AAAAGTAGTA...TAAaGATA CaTTaGGTCG TGTgTTtAAC GTTt...CTT ATTAGCACCT TAtcTAAAAG GTGGTAAAG 291 E. coli Ta cgaTGctctT gAggtgcaaa ATggtaatgA gcgtcTgGTg...TAAaGcgA CTcTGGGcCG TaTCaTgAAC GTaC...CcT gaTgtgtCCg TtCgctAAgG GcGGTAAAG —^(f) L. monocytogenes Ta tAaatctgAT gcAgAaGaaG caccaaCtag ccAAcTtact...TAcaGtaA CTcTtGGTCG TGTaTTtAAt GTat...CTT gcTAGCtCCT TACTTAAAAG GTGGTAAAa 324 S. aureus gT tATTGatgtg cctAAaGaaG AaggtaCAat AcAAcTAacA...TgAtGAaA CaTTaGGTCG TGTaTTtAAt GTaC...tTT AcTAGCACCT TAtaTtAAAG GTGGTAAAa 366 S. epidermidis ca cATcGaagtT cctAAaGaaG ATggagCgCt tcAAtTAacA...TgAcGtaA CTcTaGGaaG aGTgTTtAAC GTaC...CTT ATTAGCACCT TACaTAAAAG GTGGTAAAa 370 Selected sequences        ATTGTCTAT AAAAATGGCG ATAAGTC 627 for species-                   AAAATGGCG ATAAGTCACA AAAAGTA 628 specific primer Selected sequences                                                     GGATA CTTTGGGTCG TGTCTTCAAC G 625 for species-                                                                                            ATTAGCACCT TACTTAAAAG GTGGTA 626 specific primers^(g) The sequence numbering refers to the Streptococcus agalactiae tuf gene fragment (SEQ ID NO. 380). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. ^(a,d,e,f)These sequences were obtained from Genbank and have accession #: a = AB009314, d = AF001955, e = U31170, and f = V00311. ^(b,c)These sequences were obtained from genome sequencing projects, ^(g)These sequences are the reverse-complement of the selected primers.

Annex XI: Strategy for the selection of Candida albicans/dubliniensis-specific amplification primers, Candida albicans-specific hybridization probe and Candida dubliniensis-specific hybridization probe from tuf sequences. SEQ 337                             368   403                      428   460                              491 ID NO.: Accession #: C. albicans CGTC AAGAAGGTTG GTTACAACCC AAAGACTG...CAACATGA TTGAA C C A TC CACCAACT...C AAATCCGGTA AAGTTACTGG TAAGACCTTG T 624 — C. albicans CGTC AAGAAGGTTG GTTACAACCC AAAGACTG...CAACATGA TTGAA C C A TC CACCAACT...C AAATCCGGTA AAGTTACTGG TAAGACCTTG T 409 — C. albicans CGTC AAGAAGGTTG GTTACAACCC AAAGACTG...CAACATGA TTGAA C C A TC CACCAACT...C AAATCCGGTA AAGTTACTGG TAAGACCTTG T 410 — C. albicans CGTC AAGAAGGTTG GTTACAACCC AAAGACTG...CAACATGA TTGAA C C A TC CACCAACT...C AAATCCGGTA AAGTTACTGG TAAGACCTTG T 407 — C. albicans CGTC AAGAAGGTTG GTTACAACCC AAAGACTG...CAACATGA TTGAA C C A TC CACCAACT...C AAATCCGGTA AAGTTACTGG TAAGACCTTG T 408 — C. dubliniensis CGTC AAGAAGGTTG GTTACAACCC AAAGACTG...CAACATGA TTGAAgCtTC CACCAACT...C AAATCCGGTA AgGTTACTGG TAAGACCTTG T 412 — C. dubliniensis CGTC AAGAAGGTTG GTTACAACCC AAAGACTG...CAACATGA TTGAAgCtTC CACCAACT...C AAATCCGGTA AgGTTACTGG TAAGACCTTG T 414 — C. dubliniensis CGTC AAGAAGGTTG GTTACAACCC AAAGACTG...CAACATGA TTGAAgCtTC CACCAACT...C AAATCCGGTA AgGTTACTGG TAAGACCTTG T 415 — C. glabrata CATC AAGAAGGTcG GTTACAACCC AAAGACTG...CAACATGA TTGAAgC c aC CACCAACG...C AAggCtGGTg tcGTcAagGG TAAGACCTTG T 417 — C. guilliermondii CGTC AAGAAGGTTG GTTACAACCC tAAGACTG...CAACATGA TTGAggCtTC tACCAACT...C AAggCtGGTA AgtccACcGG TAAGACtTTG T 418 — C. kefyr CATC AAGAAGGTcG GTTACAACCC AAAGAATG...CAACATGA TTGAAgC c aC CACCAACG...C AAggCtGGTA ccGTcAagGG TAAGACCTTG T 421 — C. krusei CATC AAGAAGGTTG GTTACAACCC AAAGACTG...CAACATGA TTGAAgC A TC CACCAACT...C AAggCaGGTg ttGTTAagGG TAAGACCTTA T 422 — C. lusitaniae CGTC AAGAAGGTTG GTTACAACCC tAAGACTG...CAACATGA TTGAg C C A TC YACCAACT...C AAgTCYGGTA AgtccACcGG TAAGACCTTG T 424 — C. neoformans CATC AAGAAGGTTG GTTACAACCC cAAGgCTG...CAACATGt TgGAgg ag aC CACCAAGT...C AAgTCtGGTg tttccAagGG TAAGACCcTC C 623 — C. parapsilosis CGTC AAGAAGGTTG GTTACAACCC tAAagCTG...CAAtATGA TTGAA C C A TC aACCAACT...T AAAgCtGGTA AgGTTACcGG TAAGACCTTG T 426 — C. tropicalis CGTC AAGAAGGTTG GTTACAACCC tAAGgCTG...CAACATGA TTGAAgCtTC tACCAACT...C AAggCtGGTA AgGTTACcGG TAAGACtTTG T 429 — A. fumigatus CATC AAGAAGGTcG GcTACAACCC cAAGgCCG...CAACATGc TTGAg C C c TC CtCCAACT...C AAggCCGGcA AgGTcACTGG TAAGACCcTC A 404 — Human CATt AAGAAaaTTG GcTACAACCC cgAcACAG...CAACATGc TgGAgCCAag tgCtAACA...T AAggatGGcA AtGccAgTGG aAccACgcTG C — X03558 P. anomala TATC AAGAAaGTTG GTTACAACCC AAAaACTG...TAACATGA TTGAA C C A TC aWCtAACT...C AAAgCtGGTg AAGcTAaaGG TAAaACtTTA T 447 — S. cerevisiae TATC AAGAAGGTTG GTTACAACCC AAAGACTG...CAACATGA TTGAAgCtaC CACCAACG...C AAggCCGGTg tcGTcAagGG TAAGACtTTG T 622 — S. pombe CATC AAGAAGGTcG GTTtCAACCC cAAGACCG...TAACATGA TTGAg C C c aC CACCAACA...C AAggCtGGTg tcGTcAagGG TAAGACtcTT T — U42189 Selected sequence    C AAGAAGGTTG GTTACAACCC AAAGA for species-specific amplification primer^(a) Selected sequence                                                                         ATCCGGTA AAGTTACTGG TAAGACCT for species-specific amplification primer^(a,b) Selected sequences                                          CATGA TTGAACCATC CACCA (C. albicans) 577 for species-specific                                          CATGA TTGAAGCTTC CACCA (C. dubliniensis) 578 hybridization probes The sequence numbering refers to the Candida albicans tuf gene fragment (SEQ ID NO. 408). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches for SEQ ID NO. 577 are indicated by lower-case letters. Mismatches for SEQ ID NO. 578 are indicated by underlined nucleotides. Dots indicate gaps in the sequerices displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a) C. albicans primers have been described in a previous patent (publication WO98/20157, SEQ ID NOs. 11-12) ^(b)This sequence is the reverse-complement of the selected primer.

Annex XII: Strategy for the selection of Staphylococcus-specific amplification primers from tuf sequences. SEQ ID Accession 310                            340   652                            682 NO.: #: S. aureus A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...CACTTACCA GAAGGTACTG AAATGGTAAT GC 179 — S. aureus A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...CACTTACC~ ~~~~~~~~~~ ~~~~~~~~~~ GC 176 — S. aureus A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...CACTTACCA GAAGGTMCTG AAATGGTAAT GC 177 — S. aureus aureus A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...CACTTACCA GAAGGTACTG AAATGGTAAT GC 180 — S. auricularis A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...ActTTACCA GAAGGTACaG AAATGGTAAT GC 181 — S. capitis A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGGTACTG AAATGGTTAT GC 182 — capitis M. caseolyticus A CTGGaCGTGT TGAgCGTGGa CAAgTtAAAG...AACTTACCA GAAGGTACTG AAATGGTAAT GC 183 — S. cohnii A CAGGgCGTGT TGAACGTGGT CAAATCAAAG...ActTTACCA GAAGGTACTG AAATGGTTAT GC 184 S. epidermidis A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~ 185 — S. epidermidis A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGGTACaG AAATGGTTAT GC 141^(a) — S. haemolyticus A CAGGCCGTGT TGAACGTGGg CAAATCAAAG...AACTTACCA GAAGGTACTG AAATGGTTAT GC 186 — S. haemolyticus A CAGGtCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAG~~~~~~ ~~~~~~~~~~ ~~ 188 — S. haemolyticus A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGGTACTG AAATGG~~~~ ~~ 189 — S. hominis A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGGTACTG AAATGGTAAT GC 191 — hominis S. hominis A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGGTACTG AAATGGTAAT GC 193 — S. hominis A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGG~~~~~ ~~~~~~~~~~ ~~ 194 — S. hominis A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGGTACTG AAATGGTAAT GC 195 — S. hominis A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGGTACTG AAATGGTAAT GC 196 — S. lugdunensis A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGGTACaG AAATGGTTAT GC 197 — S. saprophyticus A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~ 198 — S. saprophyticus A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGGTACTG AAATGGTTAT GC 199 — S. saprophyticus A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...AACTTACCA GAAGGTACTG AAATGGTTAT GC 200 — S. sciuri sciuri A CAGGCCGTGT TGAACGTGGT CAAATCACTG...AACTTACCA GAAGGTACTG AAATGGTTAT GC 201 — S. warneri A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...CAaTTACCA GAAGGTACTG ~~~~~~~~~~ ~~ 187 — S. warneri A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~~~~ ~~ 192 — S. warneri A CAGGCCGTGT TGAACGTGGT CAAATCAAAG...CAaTTACCA GAAGGTACTG AAATGGTTAT GC 202 — B. subtilis A CTGGCCGTGT aGAACGcGGa CAAgTtAAAG...CAtcTtCCA GAAGGcgtaG AAATGGTTAT GC — Z99104 E. coli A CCGGtCGTGT aGAACGcGGT atcATCAAAG...GAacTgCCg GAAGGcgtaG AgATGGTAAT GC  78 — L. monocytogenes A CTGGaCGTGT TGAACGTGGa CAAgTtAAAG...AcacTtCCA GAAGGTACTG AAATGGTAAY GC 138^(a) — Selected     GGCCGTGT TGAACGTGGT CAAATCA 553 sequence for genus- specific primer Selected                                         TTACCA GAAGGTACTG AAATGGTIA 575 sequences                                         TTACCA GAAGGTACTG AAATGCTWA 707 for genus- specific primers^(b) The sequence numbering refers to the Staphylococcus aureus tuf gene fragment (SEQ ID NO. 179). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. “~” indicate incomplete sequence data. Dots indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)The SEQ ID NO. refers to previous patent publication WO98/20157. ^(b)These sequences are the reverse-complement of the selected primers.

Annex XIII: Strategy for the selection of the Staphylococcus-specific hybridization probe from tuf sequences. 400                       425 SEQ ID NO.: Accession #: S. aureus G TTGAAATGTT CCGTAAATTA TTAGA 179 — S. aureus G TTGAAATGTT CCGTAAATTA TTAGA 176 — S. aureus G TTGAAATGTT CCGTAAATTA TTAGA 177 — S. aureus G TTGAAATGTT CCGTAAATTA TTAGA 178 — S. aureus aureus G TTGAAATGTT CCGTAAATTA TTAGA 180 — S. auricularis G TAGAAATGTT CCGTAAATTA TTAGA 181 — S. capitis capitis G TAGAAATGTT CCGTAAATTA TTAGA 182 — M. caseolyticus G TAGAAATGTT CCGTAAATTA TTAGA 183 — S. cohnii G TAGAAATGTT CCGTAAATTA TTAGA 184 — S. epidermidis G TAGAAATGTT CCGTAAATTA TTAGA 185 — S. haemolyticus G TAGAAATGTT CCGTAAATTA TTAGA 186 — S. haemolyticus G TAGAAATGTT CCGTAAATTA TTAGA 189 — S. haemolyticus G TAGAAATGTT CCGTAAATTA TTAGA 190 — S. haemolyticus G TAGAAATGTT CCGTAAATTA TTAGA 188 — S. hominis G TAGAAATGTT CCGTAAATTA TTAGA 196 — S. hominis G TAGAAATGTT CCGTAAATTA TTAGA 194 — S. hominis hominis G TAGAAATGTT CCGTAAATTA TTAGA 191 — S. hominis G TAGAAATGTT CCGTAAATTA TTAGA 193 — S. hominis G TAGAAATGTT CCGTAAATTA TTAGA 195 — S. lugdunensis G TAGAAATGTT CCGTAAATTA TTAGA 197 — S. saprophyticus G TAGAAATGTT CCGTAAATTA TTAGA 198 — S. saprophyticus G TAGAAATGTT CCGTAAATTA TTAGA 200 — S. saprophyticus G TAGAAATGTT CCGTAAATTA TTAGA 199 — S. sciuri sciuri G TTGAAATGTT CCGTAAATTA TTAGA 201 — S. warneri G TAGAAATGTT CCGTAAgTTA TTAGA 187 — S. warneri G TAGAAATGTT CCGTAAgTTA TTAGA 192 — S. warneri G TAGAAATGTT CCGTAAgTTA TTAGA 202 — S. warneri G TAGAAATGTT CCGTAAgTTA TTAGA 203 — B. subtilis G TTGAAATGTT CCGTAAgcTt cTTGA — Z99104 E. coli G TTGAAATGTT CCGcAAAcTg cTGGA  78 — L. monocytogenes G TAGAAATGTT CCGTAAATTA cTAGA  138^(a) — Selected sequence for     GAAATGTT CCGTAAATTA TT 605 genus-specific hybridization probe The sequence numbering refers to the Staphylococcus aureus tuf gene fragment (SEQ ID NO. 179). Nucleotides in capitals are identical to the selected sequence or match that sequence. Mismatches are indicated by lower-case letters. ^(a)The SEQ ID NO. refers to previous patent publication WO98/20157.

Annex XIV: Strategy for the selection of Staphylococcus saprophyticus-specific and of Staphylococcus haemolyticus-specific hybridization probes from tuf sequences. SEQ ID 339                                            383 NO.: S. aureus AG TtGGTGAAGA AgTtGAAATC ATcGGTtTaC ATGACACaTC TAA 179 S. aureus AG TtGGTGAAGA AgTtGAAATC ATcGGTtTaC ATGACACaTC TAA 176 S. aureus AG TtGGTGAAGA AgTtGAAATC ATcGGTtTaC ATGACACaTC TAA 177 S. aureus AG TtGGTGAAGA AgTtGAAATC ATcGGTtTaC ATGACACaTC TAA 178 S. aureus aureus AG TtGGTGAAGA AgTtGAAATC ATcGGTtTaC ATGACACaTC TAA 180 S. auricularis AG TCGGTGAAGA AgTtGAAATC ATcGGTATga AaGACggTTC AAA 181 S. capitis capitis AG TtGGTGAAGA AgTtGAAATC ATcGGTATCC AcGAaACTTC TAA 182 M. caseolyticus AG TtGGTGAAGA AgTtGAAATC ATTGGTtTaa cTGAagaacC AAA 183 S. cohnii AG TCGGTGAAGA AgTtGAAATC ATcGGTATgC AaGAagaTTC CAA 184 S. epidermidis AG TtGGTGAAGA AgTtGAAATC ATcGGTATgC AcGAaACTTC TAA 185 S. haemolyticus AG TtGGTGAAGA AgTtGAAATC ATTGGTATCC ATGACACTTC TAA 186 S. haemolyticus AG TtGGTGAAGA AgTtGAAATC ATTGGTATCC ATGACACTTC TAA 189 S. haemolyticus AG TtGGTGAAGA AgTtGAAATC ATTGGTATCC ATGACACTTC TAA 190 S. haemolyticus AG TtGGTGAAGA AgTtGAAATt ATTGGTATCa AaGAaACTTC TAA 188 S. hominis AG TtGGTGAAGA AgTtGAAATt ATTGGTATCa AaGAaACTTC TAA 194 S. hominis hominis AG TtGGTGAAGA AgTtGAAATt ATTGGTATCa AaGAaACTTC TAA 191 S. hominis AG TtGGTGAAGA AgTtGAAATt ATTGGTATCa AaGAaACTTC TAA 193 S. hominis AG TtGGTGAAGA AgTtGAAATt ATTGGTATCa AaGAaACTTC TAA 195 S. hominis AG TtGGTGAAGA AgTtGAAATt ATTGGTATCa AaGAtACTTC TAA 196 S. lugdunensis AG TCGGTGAAGA AgTtGAAATt ATTGGTATCC AcGAtACTaC TAA 197 S. saprophyticus AG TCGGTGAAGA AATCGAAATC ATcGGTATgC AaGAagaaTC CAA 198 S. saprophyticus AG TCGGTGAAGA AATCGAAATC ATcGGTATgC AaGAagaaTC CAA 200 S. saprophyticus AG TCGGTGAAGA AATCGAAATC ATcGGTATgC AaGAagaaTC CAA 199 S. sciuri sciuri TG TtGGTGAAGA AgTtGAAATC ATcGGTtTaa cTGAagaaTC TAA 201 S. warneri AG TtGGTGAAGA AgTtGAAATC ATcGGTtTaC ATGACACTTC TAA 187 S. warneri AG TtGGTGAAGA AgTtGAAATC ATcGGTtTaC ATGACACTTC TAA 192 S. warneri AG TtGGTGAAGA AgTtGAAATC ATcGGTtTaC ATGACACTTC TAA 202 S. warneri AG TtGGTGAAGA AgTtGAAATC ATcGGTtTaC ATGACACTTC TAA 203 B. subtilis AG TCGGTGAcGA AgTtGAAATC ATcGGTcTtC AaGAagagag AAA —^(a) E. coli AG TtGGTGAAGA AgTtGAAATC gTTGGTATCa AaGAgACTca GAA  78 L. monocytogenes AG TtGGTGAcGA AgTaGAAgTt ATcGGTATCg AaGAagaaag AAA 138^(b) Selected sequences for    CGGTGAAGA AATCGAAATC A (S. saprophyticus) 599 species-specific (S. haemolyticus)        ATTGGTATCC ATGACACTTC 594 hybridization probes The sequence numbering refers to the Staphylococcus aureus tuf gene fragment (SEQ ID NO. 179). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. ^(a)This sequence was obtained from Genbank accession #Z99104. ^(b)The SEQ ID NO. refers to previous patent publication WO98/20157.

Annex XV: Strategy for the selection of Staphylococcus aureus-specific and of Staphylococcus epidermidis-specific hybridization probes from tuf sequences. SEQ ID 521                      547   592                      617 NO.: S. aureus TACACCACA TACTGAATTC AAAGCAG...TTCTTCtCa AACTA TCGtC CACAAAT 179 S. aureus TACACCACA TACTGAATTC AAAGCAG...TTCTTCtC~ ~~~~~~~~~~ ~~~~~~~ 178 S. aureus TACACCACA TACTGAATTC AAAGCAG...TTCTTCtCa AACTA TCGtC CACAAAT 176 S. aureus TACACCACA TACTGAATTC AAAGCAG...TTCTTCtCa AACTA TCGtC CACAAAT 177 S. aureus aureus TACACCACA TACTGAATTC AAAGCAG...TTCTTCtCa AACTA TCGtC CACAAAT 180 S. auricularis TACACCACA cACTaAATTC ActGCAG...TTCTTCtCT AACTA cCGtC CACAAAT 181 S. capitis capitis CACACCACA cACTaAATTC AAAGCGG...TTCTTCAgT AACTA cCGCC CACAAAT 182 M. caseolyticus TACtCCACA TACTaAATTC AAAGCTG...TTCTTCACT AACTA cCGCC CtCAGTT 183 S. cohnii TACACCACA cACaaAcTTt AAAGCGG...TTCTTCAgT AACTA TCGCC CACAAAT 184 S. epidermidis TACACCACA cACaaAATTC AAAGCTG...TTCTTCACT AACTA TCGCC CACAAAT 185 S. haemolyticus CACACCtCA cACaaAATTt AAAGCAG...TTCTTCACa AACTA TCGtC CACAAAT 186 S. haemolyticus CACACCtCA cACaaAATTt AAAGCAG...TTCTTCACa AACTA TCGtC CACAAAT 189 S. haemolyticus CACACCtCA cACaaAATTt AAAGCAG...TTCTTCACa AACTA TCGtC CACAAAT 190 S. haemolyticus TACACCtCA cACaaAATTC AAAGCAG...TTCTTCACT AACTA TCGtC CACAAAT 188 S. hominis CACACCtCA cACaaAATTC AAAGCAG...TTCTTCACT AACTA TCGtC CACAAAT 195 S. hominis TACACCtCA cACaaAATTC AAAGCAG...TTCTTCACT AACTA TCGtC CACAAAT 196 S. hominis hominis TACACCtCA cACaaAATTC AAAGCAG...TTCTTCtCT AACTA TCGtC CACAAAT 191 S. hominis TACACCtCA cACaaAATTC AAAGCAG...TTCTTCtCT AACTA TCGtC CACAAAT 193 S. hominis TACACCtCA cACaaAATTC AAAGCAG...TTCTTCtCT AACTA TCGtC CACAAAT 194 S. lugdunensis TACACCtCA cACTaAATTt AAAGCTG...TTCTTCtCa AACTA cCGCC CACAAAT 197 S. saprophyticus TACACCACA TACaaAATTC AAAGCGG...TTCTTCACT AACTA cCGCC CACAAAT 198 S. saprophyticus TACACCACA TACaaAATTC AAAGCGG...TTCTTCACT AACTA cCGCC CACAAAT 199 S. saprophyticus TACACCACA TACaaAATTC AAAGCGG...TTCTTCACT AACTA cCGCC CACAAAT 200 S. sciuri sciuri CACACCtCA cACTaAATTC AAAGCTG...TTCTTCACa AACTA cCGCC CACAAAT 201 S. warneri TACACCACA TACaaAATTC AAAGCGG...~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ 192 S. warneri TACACCACA TACaaAATTC AAAGCGG...TTCTTCAgT AACTA cCGCC CACAAAT 187 S. warneri TACACCACA TACaaAATTC AAAGCGG...TTCTTCAgT AACTA cCGCC CACAAAT 202 S. warneri TACACCACA TACaaAATTC AAAGCGG...TTCTTCAgT AACTA cCGCC CACAAAT 203 B. subtilis CACtCCACA cAgcaAATTC AAAGCTG...TTCTTCtCT AACTA cCGtC CtCAGTT —^(a) E. coli CAAgCCgCA cACcaAgTTC gAAtCTG...TTCTTCAaa ggCTA cCGtC CgCAGTT  78 L. monocytogenes TACtCCACA cACTaAcTTC AAAGCTG...TTCTTCAac AACTA cCGCC CACAAAT 138^(b) Selected sequences    ACCACA TACTGAATTC AAAG (S. aureus) 585 for species-specific (S. epidermidis)                 TTCACT AACTATCGCC CACA 593 hybridization probes The sequence numbering refers to the Staphylococcus aureus tut gene fragment (SEQ ID NO. 179). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. “~” indicate incomplete sequence data. Dots indicate gaps in the sequences displayed. ^(a)This sequence was obtained from Genbank accession #Z99104. ^(b)The SEQ ID NO. refers to previous patent publication WO98/20157.

Annex XVI: Strategy for the selection of the Staphylococcus hominis-specific hybridization probe from tuf sequences. 358                       383 SEQ ID NO.: S. aureus ATC ATcGGTtTac AtGAcACaTC TAA 179 S. aureus ATC ATcGGTtTac AtGAcACaTC TAA 176 S. aureus ATC ATcGGTtTac AtGAcACaTC TAA 177 S. aureus ATC ATcGGTtTac AtGAcACaTC TAA 178 S. aureus aureus ATC ATcGGTtTac AtGAcACaTC TAA 180 S. auricularis ATC ATcGGTATgA AAGAcggTTC AAA 181 S. capitis capitis ATC ATcGGTATCc AcGAAACTTC TAA 182 M. caseolyticus ATC ATTGGTtTaA ctGAAgaacC AAA 183 S. cohnii ATC ATcGGTATgc AAGAAgaTTC CAA 184 S. epidermidis ATC ATcGGTATgc AcGAAACTTC TAA 185 S. haemolyticus ATC ATTGGTATCc AtGAcACTTC TAA 186 S. haemolyticus ATC ATTGGTATCc AtGAcACTTC TAA 189 S. haemolyticus ATC ATTGGTATCc AtGAcACTTC TAA 190 S. haemolyticus ATT ATTGGTATCA AAGAAACTTC TAA 188 S. hominis ATT ATTGGTATCA AAGAtACTTC TAA 196 S. hominis ATT ATTGGTATCA AAGAAACTTC TAA 194 S. hominis hominis ATT ATTGGTATCA AAGAAACTTC TAA 191 S. hominis ATT ATTGGTATCA AAGAAACTTC TAA 193 S. hominis ATT ATTGGTATCA AAGAAACTTC TAA 195 S. lugdunensis ATT ATTGGTATCc AcGAtACTaC TAA 197 S. saprophyticus ATC ATcGGTATgc AAGAAgaaTC CAA 198 S. saprophyticus ATC ATcGGTATgc AAGAAgaaTC CAA 200 S. saprophyticus ATC ATcGGTATgc AAGAAgaaTC CAA 199 S. sciuri sciuri ATC ATcGGTtTaA ctGAAgaaTC TAA 201 S. warneri ATC ATcGGTtTac AtGAcACTTC TAA 187 S. warneri ATC ATcGGTtTac AtGAcACTTC TAA 192 S. warneri ATC ATcGGTtTac AtGAcACTTC TAA 202 S. warneri ATC ATcGGTtTac AtGAcACTTC TAA 203 B. subtilis ATC ATcGGTcTtc AAGAAgagag AAA —^(a) E. coli ATC gTTGGTATCA AAGAgACTca GAA  78 L. monocytogenes GTT ATcGGTATCg AAGAAgaaag AAA 138^(b) Selected sequence for     ATTGGTATCA AAGAAACTTC 597 species-specific hybridization probe The sequence numbering refers to the Staphylococcus aureus tuf gene fragment (SEQ ID NO. 179). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. ^(a)This sequence was obtained from Genbank accession #Z99104. ^(b)The SEQ ID NO. refers to previous patent publication WO98/20157.

Annex XVII: Strategy for the selection of the Enterococcus-specific amplification primers from tuf sequences. SEQ ID Accession 270                         298   556                        582 NO.: #: E. avium TAGAATTAAT GGCTGCTGTT GACGAATAT...TGAA GATATCCAAC GTGGACAAGTATT  131^(a) — E. casseliflavus TGGAATTAAT GGCTGCAGTT GACGAATAC...TGAA GACATCCAAC GTGGACAAGT ATT  58 — E. cecorum TAGAATTAAT GGCTGCAGTT GACGAATAC...TGAA GATATCCAAC GTGGtCAAGT ATT  59 — E. dispar TAGAATTAAT GGCTGCAGTT GACGAATAT...TGAA GATATCCAAC GTGGtCAAGT ATT  60 — E. durans TTGAATTAAT GGCTGCAGTT GACGAATAT...TGAA GACATCCAAC GTGGACAAGT TTT  61 — E. flavescens TGGAATTAAT GGCTGCAGTT GACGAATAC...TGAA GACATCCAAC GTGGACAAGT ATT  65 — E. faecium TTGAATTAAT GGCTGCAGTT GACGAATAC...TGAA GACATCCAAC GTGGACAAGT TTT  608 — E. faecalis TAGAATTAAT GGCTGCAGTT GACGAATAT...TGAA GATATCGAAC GTGGACAAGT ATT  607 — E. gallinarum TGGAATTgAT GGCTGCAGTT GACGAATAC...TGAA GACATCCAAC GTGGACAAGT ATT  609 — E. hirae TTGAATTgAT GGCTGCAGTT GACGAATAT...TGAA GACATCCAAC GTGGACAAGT TTT  67 — E. mundtii TTGAATTgAT GGCTGCAGTT GACGAATAT...TGAA GACATCCAAC GTGGtCAAGT TTT  68 — E. pseudoavium TAGAATTAAT GSCTGCTGTT GACGAATAC...TGAA GACATCCAAC GTGGACAAGT ATT  69 — E. raffinosus TAGAATTAAT GGCTGCTGTT GATGAATAC...TGAA GACATCCAAC GTGGACAAGT ATT  70 — E. saccharolyticus TCGAATTAAT GGCTGCAGTT GACGAATAT...TGAA GACATCCAAC GTGGACAAGT ATT  71 — E. solitarius TGGAcTTAAT GGaTGCAGTT GATGAcTAC...TGAt GATATCGAAC GTGGtCAAGT ATT  72 — E. coli TGGAAcTggc tGgcttccTg GATtctTAY...TGAA GAaATCGAAC GTGGtCAgGT ACT  78 — B. cepacia TGAgccTggc cGacGCgcTg GACacgTAC...TGAA GACgTgGAgC GTGGcCAgGT TCT  16 — B. fragilis TGGAAcTgAT GGaaGCTGTT GATactTGG...GAAc GAaATCaAAC GTGGtatgGT TCT — M22247 B. subtilis TCGAAcTtAT GGaTGCgGTT GATGAgTAC...TGAA GAaATCCAAC GTGGtCAAGT ACT — Z99104 C. diphtheriae TCGAccTcAT GcagGCTtgc KATGAtTCC...CGAA GACgTtGAgC GTGGcCAgGT TGT  662 — C. trachomatis GAGAgcTAAT GcaaGCcGTc GATGAtAAT...GAAc GATgTgGAAa GaGGAatgGT TGT  22 — G. vaginalis AGGAAcTcAT GaagGCTGTT GACGAgTAC...TACc GACgTtGAgC GTGGtCAgGT TGT  135^(a) — S. aureus TAGAATTART GGaaGCTGTa GATactTAC...TGAA GACgTaCAAC GTGGtCAAGT ATT  179 — S. pneumoniae TGGAATTgAT GaacaCAGTT GATGAgTAT...TGAt GAaATCGAAC GTGGACAAGT TAT  145^(a) — A. adiacens TAGAATTAAT GGCTGCTGTT GACGAATAC...TGAA aACATCGAAC GTGGACAAGT TCT  118^(a) — G. haemolysans TCGAATTAAT GGaaaCAGTT GACGAATAC...TGAA GACATCGAAC GTGGACAAGT TTT  87 — G. morbillorum TCGAATTAAT GGaaaCAGTT GACGAgTAC...TGAA GATATCGAAC GTGGACAAGT TTT  88 — Selected sequence for    AATTAAT GGCTGCWGTT GAYGAA 1137 amplification primer Selected sequence for                                     A GAYATCSAAC GTGGACAAGT 1136 amplification primer^(b) The sequence numbering refers to the Enterococcus durans tuf gene fragment (SEQ ID NO. 61). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. “Y” “W” and “S” designate nucleotide positions which are degenerated. “Y” stands for C or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)The SEQ ID NO. refers to previous patent publication WO98/20157. ^(b)This sequence is the reverse-complement of the selected primer.

Annex XVIII: Strategy for the selection of the Enterococcus faecalis-specific hybridization probe, of the Enterococcus faecium-specific hybridization probe and of the Enterococcus casseliflavus-flavescens-gallinarum group-specific hybridization probe from tuf sequences. 395                                                     448...526                    549 SEQ ID NO.: Accession #: E. avium GTTGA ACGTGGacAA GTTCGCGTTG GTGACGAAGT TGAAaTcGTa GGTATcGCT...CATc GGTGCtTTGt TACGTGGTGT 131^(a) — E. casseliflavus GTTGA ACGTGGacAA GTTCGCGTTG GTGACGAAGT TGAAaTcGTT GGTATTGCT...CATT GGTGCATTGC TACGTGGTGT 58 — E. cecorum GTTGA ACGTGGacAA GTaCGtGTTG GTGACGAAGT TGAAaTaGTT GGTATcCAT...CATc GGTGCATTat TACGTGGTGT 59 — E. dispar GTTGA ACGTGGacAA GTTCGCGTTG GTGACGAAGT TGAAaTcGTa GGTATcGCT...CATT GGTGCATTat TACGTGGTGT 60 — E. durans GTTGA ACGTGGacAA GTTCGCGTTG GTGACGttGT aGAtaTcGTT GGTATcGCA...CATT GGTGCtTTaC TACGTGGTGT 61 — E. faecalis GTTGA ACGTGGTGAA GTTCGCGTTG GTGACGAAGT TGAAaTcGTT GGTATTAAA...CTTc GGTGCtTTat TACGTGGTGT 62 — E. faecium GTTGA ACGTGGacAA GTTCGCGTTG GTGACGAAGT TGAAGTTGTT GGTATTGCT...CATT GGTGCtTTaC TACGTGGTGT 608  — E. flavescens GTTGA ACGTGGacAA GTTCGCGTTG GTGACGAAGT TGAAaTcGTT GGTATTGCT...CATT GGTGCATTGC TACGTGGGGT 65 — E. gallinarum GTTGA ACGTGGacAA GTTCGCGTTG GTGATGAAGT aGAAaTcGTT GGTATTGCT...CATT GGTGCATTGC TACGTGGGGT 609  — E. hirae GTTGA ACGTGGacAA GTTCGCGTTG GTGACGttGT aGAtaTcGTT GGTATcGCA...CATT GGTGCtTTaC TACGTGGTGT 67 — E. mundtii GTTGA ACGTGGacAA GYTCGtGTTG GTGACGttaT cGAtaTcGTT GGTATcGCA...CATT GGTGCgTTaC TACGTGGTGT 68 — E. pseudoavium GTTGA ACGTGGacAA GTTCGCGTTG GTGACGAAGT TGAAaTcGTa GGTATCGCT...CATc GGTGCATTat TACGTGGTGT 69 — E. raffinosus GTTGA ACGTGGacAA GTTCGCGTTG GTGACGAAGT TGAAaTcGTa GGTATTGCT...CATT GGTGCATTat TACGTGGTGT 70 — E. saccharolyticus GTTGA ACGTGGacAA GTTCGCGTTG GTGACGttGT aGAAaTcGTT GGTATcGAC...CATc GGTGCtTTat TACGTGGGGT 71 — E. solitarius GTTGA ACGcGGgact aTcaaaGTCG GCGATGAAGT TGAcaTTaTT GGTATTCAT...CATT GGTaCtTTGt TACGTGGTGT 72 — C. diphtheriae GTTGA gCGTGGctcc cTgaagGTCA ACGAGGAcGT cGAgaTcaTc GGTATcCGC...CTGT GGTctgcTtC TcCGTGGCGT 662 — G. vaginalis GTTGA gCGTGGTaAg cTcCcaATCA ACACCCcAGT TGAgaTcGTT GGTtTgCGC...CACT GGTcttcTtC TcCGcGGTAT 135^(a) — B. cepacia GTCGA gCGcGGcatc GTgaagGTCG GCGAAGAAaT cGAAaTcGTc GGTATcAAG...CGTT GGTatccTGC TgCGcGGCAC 16 — S. aureus GTTGA ACGTGGTcAA aTcaaaGTTG GTGAAGAAGT TGAAaTcaTc GGTtTaCAT...CATT GGTGCATTat TACGTGGTGT 179  — B. subtilis GTAGA ACGcGGacAA GTTaaaGTCG GTGACGAAGT TGAAaTcaTc GGTcTTCAA...CATT GGTGCccTtC TtCGcGGTGT — Z99104 S. pneumoniae ATCGA cCGTGGTatc GTTaaaGTCA ACGACGAAaT cGAAaTcGTT GGTATcAAA...CGTa GGTGtccTtC TtCGTGGTGT 145^(a) — E. coli GTAGA ACGcGGTatc aTcaaaGTTG GTGAAGAAGT TGAAaTcGTT GGTATcAAA...CGTa GGTGttcTGC TgCGTGGTAT 78 — B. fragilis ATCGA AacTGGTGtt aTcCatGTAG GTGATGAAaT cGAAaTccTc GGTtTgGGT...CGTa GGTctgTTGC TtCGTGGTGT — M22247 C. trachomatis ATTGA gCGTGGaatt GTTaaaGTTT CCGATAAAGT TcAgtTgGTc GGTcTTAGA...CGTT GGattgcTcC TcaGaGGTAT 22 — Selected sequences for    GA ACGTGGTGAA GTTCGC (E. faecalis) 1174   species-specific or                                   AAGT TGAAGTTGTT GGTATT (E. faecium) 602  group-specific                                                                  T GGTGCATTGC TACGTGG 1122   hybridization probes The sequence numbering refers to the Enterococcus faecium tuf gene fragments (SEQ ID NO. 608). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. ^(a)The SEQ ID NO. refers to previous patent publication WO98/20157.

Annex XIX: Strategy for the selection of primers for the identification of platelets contaminants from tuf sequences. SEQ Accession 467                          495   689                          717 ID NO.: #: B. cereus GTA ACTGGTGTaG AGATGTTCCG TAAACT...C AGTTCTACTT CCGTACAACT GACGTAAC   7 — B. subtilis GTT ACaGGTGTTG AAATGTTCCG TAAGCT...C AGTTCTACTT CCGTACAACT GACGTAAC — Z99104 E. cloacae TGT ACTGGCGTTG AAATGTTCCG CAAACT...C AGTTCTACTT CCGTACAACT GACGTGAC  54 — E. coli TGT ACTGGCGTTG AAATGTTCCG CAAACT...C AGTTCTACTT CCGTACTACT GACGTGAC  78 — K. oxytoca TGT ACTGGCGTTG AAATGTTCCG CAAACT...C AGTTCTACTT CCGTACAACT GACGTGAC 100 — K. pneumoniae TGT ACTGGCGTTG AAATGTTCCG CAAACT...C AGTTCTACTT CCGTACTACT GACGTGAC 103 — P. aeruginosa TGC ACcGGCGTTG AAATGTTCCG CAAGCT...C AGTTCTACTT CCGTACCACK GACGTGAC 153 — S. agalactiae GTT ACTGGTGTTG AAATGTTCCG TAAACA...C AATTCTACTT CCGTACAACT GACGTAAC 209 — S. aureus GTT ACaGGTGTTG AAATGTTCCG TAAATT...C AATTCTATTT CCGTACTACT GACGTAAC  140^(a) — S. choleraesuis TGT ACTGGCGTTG AAATGTTCCG CAAACT...C AGTTCTACTT CCGTACTACT GACGTGAC 159 — S. epidermidis GTT ACTGGTGTaG AAATGTTCCG TAAATT...C AATTCTATTT CCGTACTACT GACGTAAC 611 — S. marcescens TGT ACTGGCGTTG AAATGTTCCG CAAACT...C AGTTCTACTT CCGTACCACT GACGTGAC 168 — S. mutans GTT ACTGGTGTTG AAATGTTCCG TAAACA...C AATTCTACTT CCGTACAACT GACGTAAC 224 — S. pyogenes GTT ACTGGTGTTG AAATGTTCCG TAAACA...C AATTCTACTT CCGTACAACT GACGTAAC — U40453 S. salivarius GTT ACTGGTGTTG AAATGTTCCG TAAACA...C AGTTCTACTT CCGTACAACT GACGTAAC  146^(a) — S. sanguinis GTT ACTGGTGTTG AAATGTTCCG TAAACA...C AGTTCTACTT CCGTACAACT GACGTTAC 227 — Y. enterocolitica TGT ACTGGCGTTG AAATGTTCCG CAAACT...C AGTTCTACTT CCGTACAACT GAtGTAAC 235 — Selected sequence     ACTGGYGTTG AIATGTTCCG YAA 636 for amplification primer Selected sequence                                        TTCTAYTT CCGTACIACT GACGT 637 for amplification primer^(b) The sequence numbering refers to the E. coli tuf gene fragment (SEQ ID NO. 78). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)The SEQ ID NO. refers to previous patent publication WO98/20157. ^(b)This sequence is the reverse-complement of the selected primer.

Annex XX: Strategy for the selection of the universal amplification primers from atpD sequences. 616                                        657   781                             812 SEQ ID NO. ACCESSION #: C. glutamicum GTGTTCGGTC AGATGG ATGA GCCACCAGGA GTCCGTATG CGC...CGTATg CCTTCCGCCG TGGGTTACCA GCCAAC — X76875 M. tuberculosis GTATTCGGAC AGATGG ACGA GCCGCCGGGC aCCCGTATG CGT...CGGATg CCGTCGGCCG TGGGATACCA GCCCAC — Z73419 E. faecalis GTGTTCGGAC AAATGAACGA ACCACCAGGT GCTCGGATG CGG...CGTATg CCTTCTGCCG TTGGTTACCA ACCAAC 291 — S. agalactiae GTCTTTGGTC AAATGAATGA ACCACCAGGA GCACGTATG CGT...CGTATg CCTTCAGCCG TTGGTTATCA ACCAAC 380 — B. subtilis GTATTCGGAC AAATGAACGA GCCGCCGGGC GCACGTATG CGT...CGTATg CCTTCAGCGG TTGGTTATCA GCCGAC — Z28592 L. monocytogenes GTATTCGGTC AAATGAACGA GCCACCAGGT GCGCGTATG CGT...CGTATg CCATCTGCGG TAGGTTACCA ACCAAC 324 — S. aureus GTATTCGGGC AAATGAATGA GCCACCTGGT GCACGTATG CGT...CGTATg CCTTCTGCAG TAGGTTACCA ACCAAC 366 — A. baumannii GTCTACGGTC AGATGAACGA GCCACCAGGT aaCCGTtTa CGC...CGTATg CCATCTGCGG TAGGTTACCA ACCTAC 243 — N. gonorrhoeae GTGTATGGCC AAATGAACGA ACCTCCAGGC aaCCGTcTG CGC...CGTATg CCTTCTGCAG TGGGTTACCA ACCGAC — Genome project C. freundii GTATATGGCC AGATGAACGA GCCGCCTGGA aaCCGTcTG CGT...CGTATg CCATCAGCGG TAGGCTACCA GCCGAC 264 — E. cloacae GTTTACGGCC AGATGAACGA GCCACCAGGA aaCCGTcTG CGC...CGTATg CCTTCAGCGG TAGGTTATCA GCCTAC 284 — E. coli GTGTATGGCC AGATGAACGA GCCGCCGGGA aaCCGTcTG CGC...CGTATg CCTTCAGCGG TAGGTTATCA GCCGAC 669 V00267 S. typhimurium GTGTATGGCC AGATGAACGA GCCGCCGGGA aaCCGTcTG CGC...CGTATg CCTTCCGCAG TAGGTTACCA GCCGAC 351 — K. pneumoniae GTGTACGGCC AGATGAACGA GCCGCCGGGA aaCCGTcTG CGC...CGTATg CCTTCAGCGG TAGGTTATCA GCCGAC 317 — S. marcescens GTTTACGGCC AGATGAACGA GCCACCAGGT aaCCGTcTG CGC...CGTATg CCATCCGCGG TAGGTTATCA GCCAAC 357 — Y. enterocolitica GTTTATGGCC AAATGAATGA GCCACCAGGT aaCCGTcTG CGC...CGTATg CCATCTGCCG TAGGTTACCA GCCAAC 393 — B. cepacia GTGTACGGCC AGATGAACGA GCCGCCGGGC aaCCGTcTG CGC...CGTATg CCGTCGGCAG TGGGCTATCA GCCGAC — X76877 H. influenzae GTTTATGGTC AAATGAACGA GCCACCAGGT aaCCGTtTa CGT...CGTATg CCATCCGCGG TAGGTTACCA ACCGAC — U32730 M. pneumoniae GTGTTTGGTC AGATGAACGA ACCCCCAGGA GCACGGATG CGG...CGGATg CCATCAGCCG TGGGTTACCA ACCAAC — U43738 H. pylori TGCTATGGGC AAATGAATGA GCCACCAGGT GCAAGGAat CGC...CGTAT C CCTTCAGCGG TGGGGTATCA GCCCAC 670 V00267 B. fragilis GTGTTCGGAC AGATGAACGA ACCTCCTGGA GCACGTgct TCA...CGTATg CCTTCTGCGG TAGGTTATCA ACCTAC — M22247 Selected sequences for          C ARATGRAYGA RCCICCIGGI GYIMGIATG 562 universal primers    TAYGGIC ARATGAAYGARCCICCIGGI AA 564 Selected sequences for                                                     ATH CCITCIGCIG TIGGITAYCA RCC 565 universal primers^(a)                                                     ATG CCITCIGCIG TIGGITAYCA RCC 563 The sequence numbering refers to the Escherichia coli atpD gene fragment (SEQ ID NO. 669). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches for SEQ ID NOs. 562 and 565 are indicated by lower-case letters. Mismatches for SEQ ID NOs. 564 and 563 are indicated by underlined nucleotides. Dots indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” letters designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “H” stands for A, C or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)These sequences are the reverse-complement of the selected primers.

Annex XXI: Specific and ubiquitous primers for nucleic acid amplification (recA sequences). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Universal primers (recA)  919 5′-GGI CCI GAR TCI TMI GGI AAR AC 918^(a) 437-459  920^(b) 5′-TCI CCV ATI TCI CCI TCI AIY TC 918^(a) 701-723  921 5′-TIY RTI GAY GCI GAR CAI GC 918^(a) 515-534  922^(b) 5′-TAR AAY TTI ARI GCI YKI CCI CC 918^(a) 872-894 Sequencing primers (recA) 1605 5′-ATY ATY GAA RTI TAY GCI CC 1704^(a)  220-239 1606 5′-CCR AAC ATI AYI CCI ACT TTT TC 1704^(a)  628-650 Universal primers (rad51)  935 5′-GGI AAR WSI CAR YTI TGY CAY AC 939^(a) 568-590  936^(b) 5′-TCI SIY TCI GGI ARR CAI GG 939^(a) 1126-1145 Universal primers (dmc1)  937 5′-ATI ACI GAR GYI TTY GGI GAR TT 940^(a) 1038-1060  938^(b) 5′-CYI GTI GYI SWI GCR TGI GC 940^(a) 1554-1573 ^(a)Sequences from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Annex XXII: Specific and ubiquitous primers for nucleic acid amplification (speA sequences). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial species: Streptococcus pyogenes 994 5′-TGG ACT AAC AAT CTC GCA AGA GG 993^(a) 60-82 995^(b) 5′-ACA TTC TCG TGA GTA ACA GGG T 993^(a) 173-194 996 5′-ACA AAT CAT GAA GGG AAT CAT TTA G 993^(a) 400-424 997^(b) 5′-CTA ATT CTT GAG CAG TTA CCA TT 993^(a) 504-526 998 5′-GGA GGG GTA ACA AAT CAT GAA GG 993^(a) 391-413 997^(b) 5′-CTA ATT CTT GAG CAG TTA CCA TT 993^(a) 504-526 ^(a)Sequence from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Annex XXIII: First strategy for the selection of Streptococcus pyogenes-specific amplification primers from speA sequences. ACCESSION # 57                            85   170                         197 SEQ ID NO.: speA X61573 CCTT GGgCTAACAA cCTCaCAAGA aGTAT...GTGAtCCT.GT cgtTCAtGAG AATGTAAA — speA AF029051 ~~~~ GGgCTAACAA cCTCaCAAGA aGTAT...GTGAtCCT.GT cgtTCAtGAG AATGTAAA — speA X61571 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61570 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61568 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61569 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61572 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61560 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA U40453 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA 993 speA X61554 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61557 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61559 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61558 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61556 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61555 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61560 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61561 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61566 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61567 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61562 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61563 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61564 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X61565 TCTT GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA AF055698 ~~~~ GGACTAACAA TCTCGCAAGA GGTAT...GTGACCCT.GT TACTCACGAG AATGTGAA — speA X03929^(a) TCTT GGACTAACAA TCTtGCcAaA aGGTA...GTGACCCTGGT TACTCACGAG AATGTGAA — Selected    T GGACTAACAA TCTCGCAAGA GG 994 sequence for species-specific primer Selected                                       ACCCT.GT TACTCACGAG AATGT 995 sequence for species-specific primer^(b) The sequence numbering refers to the Streptococcus pyogenes speA gene fragment (SEQ ID NO. 993). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. “~” indicate incomplete sequence data. Dots indicate gaps in the sequences displayed. ^(a)The extra G nucleotide introducing a gap in the sequence is probably a sequencing error. ^(b)This sequence is the reverse-complement of the selected primer.

Annex XXIV: Second strategy for the selection of Streptococcus pyogenes-specific amplification primers from speA sequences. SEQ ID Accession # 388                                      427   501                         529 NO.: speA X61573 TA TGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA AF029051 TA TGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61571 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61570 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61568 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61569 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61572 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61560 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA U40453 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT 993 speA X61554 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61557 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61559 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61558 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61556 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61555 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61560 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61561 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61566 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61567 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61562 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61563 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61564 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X61565 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA AF055698 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAGACT — speA X03929 TA CGGAGGGGTA ACAAATCATG AAGGGAATCA TTTAGAAA...AAAAATGGT AACTGCTCAA GAATTAG.CT — Selected     GGAGGGGTA ACAAATCATG AAGG 998 sequences for species-specific               ACAAATCATG AAGGGAATCA TTTAG 996 primers Selected                                                   AATGGT AACTGCTCAA G AATTAG 997 sequence for species-specific primer^(a) The sequence numbering refers to the Streptococcus pyogenes speA gene fragment (SEQ ID NO. 993). Dots indicate gaps in the sequences displayed. ^(a)This sequence is the reverse-complement of the selected primer.

Annex XXV: Strategy for the selection of Streptococcus pyogenes-specific amplification primers from tuf sequences. SEQ ID 140                                              186   619                          647 NO.: S. anginosus A AGTTGACtTg GTTGACGAtG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATt cAtCCACACA CTAAATT 211 S. bovis A AGTTGACCTT GTTGATGACG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATC cACCCACACA CTAAATT 212 S. dysgalactiae A AATTGACCTT GTTGAcGAtG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATC AACCCACABCA CTAAATT 217 S. pyogenes A AGTTGACCTT GTTGATGACG AAGAGTTGCT TGAATTAGTT GAGATG...CC AAGTTCAATC AACCCACABCA CTAAATT 1002  S. agalactiae A AGTTGACCTT GTTGATGAtG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATC AACCCACABCA CTAAATT  144^(a) S. oralis A AATTGACtTg GTAGAcGACG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATC AACCCACABCA CTAAATT 985 S. pneumoniae A AGTTGACtTg GTTGAcGACG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATC AACCCACABCA CTAAATT  145^(a) S. cristatus A GATCGACtTg GTTGATGACG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATC AACCCACABCA CTAAATT 215 S. mitis A GATCGACtTg GTTGATGACG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATC AACCCACABCA CTAAATT 982 S. gordonii A AGTTGACtTg GTTGAcGAtG AAGAaTTGCT TGAGTTgGTT GAaATG...CC AgGTTCAATC AACCCACABCA CTAAATT 200 S. sanguinis A AGTTGACtTg GTTGAcGAtG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATC AACCCACABCA CTAAATT 227 S. parasanguinis A AGTTGACtTg GTTGATGAtG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATC AACCCACABCA CTAAATT 225 S. salivarius A AGTTGACtTg GTTGAcGAtG AAGAaTTGCT TGAATTgGTT GAaATG...CC TgGTTCAATC AACCCACABCA CTAAATT  146^(a) S. vestibularis A AGTTGACtTg GTTGAcGAtG AAGAaTTGCTTGAATTgGTT GAaATG.. CC TgGTTCAATC AACCCACABCA CTAAATT 231 S. suis A AGTTGACtTg GTTGAcGAtG AAGAaTTGCT TGAgTTgGTT GAaATG...CC AgGTTCtATC AACCCACABCA CTAAATT 229 S. mutans A AGTTGAttTg GTTGAcGAtG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGTTCAATt cACCCACACA CTAAATT 224 S. ratti A GGTTGACtTg GTTGATGAtG AAGAa TTGCT TGAATTgGTT GAaATG...CC AgGTTCAATt cAtCCgCAcA CTAAATT 226 S. macacae A AGTTGACtTa GTTGATGAtG AAGAaTTGCT TGAATTgGTT GAaATG...CC AgGATCAATt cAtCCACAcA CTAAATT 222 S. cricetus A GGTTGACtTg GTTGAcGAtG AAGAaTTGCT TGAATTgGTT GAaATG...CC TgGTTCAATC cAtCCACACA CTAAATT 214 E. faecalis A AATgGAtaTg GTTGATGACG AAGAaTTatT aGAATTAGTa GAaATG...CC AgcTaCAATC ActCCACACA CaAAATT 607 S. aureus A AGTTGACaTg GTTGAcGAtG AAGAaTTatT aGAATTAGTa GAaATG...CC TgGTTCAATt AcaCCACACA CTgAATT 176 B. cereus A ATgcGACaTg GTaGATGACG AAGAaTTatT aGAATTAGTa GAaATG...AG CgGTTCtgTa AAagCtCACg CTAAATT   7 E. coli A ATgcGACaTg GTTGATGACG AAGAGcTGCT gGAAcTgGTT GAaATG...CC GgGCaCcATC AAgCCgCACA CcAAGTT  78 Selected sequences for species-specific     TTGACCTT GTTGATGACG AAGAG 999 primers                         AAGAGTTGCT TGAATTAGTT GAG 1001  Selected sequence for species-specific primer                                                            AGTTCAATC AACCCACABCA CTAA 1000  ^(b) The sequence numbering refers to the Streptococcus pyogenes tuf gene fragment (SEQ ID NO. 1002). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. ^(a)The SEQ ID NO. refers to previous patent publication WO98/20157. ^(b)This sequence is the reverse-complement of the selected primer.

Annex XXVI: Strategy for the selection stx₁-specific amplification primers and hybridization probe. SEQ ID Accession # 230                               263   343                              375   391                            421 NO.: stx₁ M19473a TTGATGTC AGAGGGATAG ATCCAGAGGA AGGGCG...TATCG CTTTGCTGAT TTTTCACATG TTACCTTT...GTTACAT TGTCTGGTGA CAGTAGCTAT ACCA — stx₁ M16625 TTGATGTC AGAGGGATAG ATCCAGAGGA AGGGCG...TATCG CTTTGCTGAT TTTTCACATG TTACCTTT...GTTACAT TGTCTGGTGA CAGTAGCTAT ACCA — stx₁ M17358 TTGATGTC AGAGGGATAG ATCCAGAGGA AGGGCG...TATCG CTTTGCTGAT TTTTCACATG TTACCTTT...GTTACAT TGTCTGGTGA CAGTAGCTAT ACCA — stx₁ Z36900 TTGATGTC AGAGGGATAG ATCCAGAGGA AGGGCG...TATCG CTTTGCTGAT TTTTCACATG TTACCTTT...GTTACAT TGTCTaGTGA CAGTAGCTAT ACCA — stx₁ L04539 TTGATGTC AGAGGGATAG ATCCAGAGGA AGGGCG...TATCG CTTTGCTGAT TTTTCACATG TTACCTTT...GTTACAT TGTCTGGTGA CAGTAGCTAT ACCA — stx₁ M19437 TTGATGTC AGAGGGATAG ATCCAGAGGA AGGGCG...TATCG CTTTGCTGAT TTTTCACATG TTACCTTT...GTTACAT TGTCTGGTGA CAGTAGCTAT ACCA — stx₁ M24352 TTGATGTC AGAGGGATAG ATCCAGAGGA AGGGCG...TATCG CTTTGCTGAT TTTTCACATG TTACCTTT...GTTACAT TGTCTGGTGA CAGTAGCTAT ACCA — stx₁ X07903 TTGATGTC AGAGGGATAG ATCCAGAGGA AGGGCG...TATCG CTTTGCTGAT TTTTCACATG TTACCTTT...GTTACAT TGTCTGGTGA CAGTAGCTAT ACCA — stx₁ Z36899 TTGATGTC AGAGGGATAG ATCCAGAGGA AGGGCG...TATCG CTTTGCTGAT TTTTCACATG TTACCTTT...GTTACAT TGTCTGGTGA CAGTAGCTAT ACCA — stx₁ Z36901 TTGATGTC AGAGGGATAG ATCCAGAGGA AGGGCG...TATCG CTTTGCTGAT TTTTCACATG TTACCTTT...GTTACAT TGTCTGGTGA CAGTAGCTAT ACCA 1076 stx₂ X61283 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ L11079 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ M21534 TAGgTaTa cGAGGGcTtG ATgtttAtcA gGaGCG...TACaG aTTTtCaGAT TTTgCACATa TatCaTTG...ATTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ M36727 TAGgTaTa cGAGGGcTtG ATgtttAtcA gGaGCG...TACaG aTTTtCaGAT TTTgCACATa TatCaTTG...ATTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ X81415 TAGgTaTa cGAGGGcTtG ATgtttAtcA gGaGCG...TACaG aTTTtCaGAT TTTgCACATa TatCaTTG...ATTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ X81416 TAGgTaTa cGAGGGcTtG ATgtttAtcA gGaGCG...TACaG aTTTtCaGAT TTTgCACATa TatCaTTG...ATTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ X81417 TAGgTaTa cGAGGGcTtG ATgtttAtcA gGaGCG...TACaG aTTTtCaGAT TTTgCACATa TatCaTTG...ATTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ X81418 TAGgTaTa cGAGGGcTtG ATgtttAtcA gGaGCG...TACaG aTTTtCaGAT TTTgCACATa TatCaTTG...ATTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ E03962 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ E03959 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ X07865 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ Y10775 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ Z37725 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA 1077 stx₂ Z50754 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ X67514 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ L11078 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ X65949 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACCG tTTTtCaGAT TTTaCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — stx₂ AF043627 TGGATaTa cGAGGGcTtG ATgtctAtcA gGcGCG...TACaG aTTTtCaGAT TTTgCACATa TatCaGTG...GTTtCca TGaCaacgGA CAGcAGtTAT ACCA — Selected sequence for    ATGTC AGAGGGATAG ATCCAGAGGA AGG 1081 amplification primer Selected sequence for                                            CG CTTTGCTGAT TTTTCACATG TTACC 1084 hybridization probe Selected sequence for                                                                                 ACAT    TGTCTGGTGA     CAGTAGCTAT A 1080 amplification primer^(a) The sequence numbering refers to the Escherichia coli stx₁ gene fragment (SEQ ID NO. 1076). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. ^(a)This sequence is the reverse-complement of the selected primer.

Annex XXVII: Strategy for the selection of stx₂-specific amplification primers and hybridization probe. Accession # 543                         570   614                            641   684                      708 SEQ ID NO.: stx₁ M19473 AGCga TgtTaCGgTT TGTtACTGTG ACA...CAAC ACTGgaTGAt ctcAgTGggC gTtcTTA...A AGgtTgAGtA gCGTcCTgCC tGAC — stx₁ M16625 AGCga TgtTaCGgTT TGTtACTGTG ACA...CAAC ACTGgaTGAt ctcAgTGggC gTtcTTA...A AGgtTgAGtA gCGTcCTgCC tGAC — stx₁ M17358 AGCga TgtTaCGgTT TGTtACTGTG ACA...CAAC ACTGgaTGAt ctcAgTGggC gTtcTTA...A AGgtTgAGtA gCGTcCTgCC tGAC — stx₁ Z36900 AGCga TgtTaCGgTT TGTtACTGTG ACA...CAAC ACTGgaTGAt ctcAgTGggC gTtcTTA...A AGgtTgAGtA gTGTcCTgCC tGAT — stx₁ L04539 AGCga TgtTaCGgTT TGTtACTGTG ACA...CAAC ACTGgaTGAt ctcAgTGggC gTtcTTA...A AGgtTgAGtA gTGTcCTgCC tGAT — stx₁ M19437 AGCga TgtTaCGgTT TGTtACTGTG ACA...CAAC ACTGgaTGAt ctcAgTGggC gTtcTTA...A AGgtTgAGtA gTGTcCTgCC tGAC — stx₁ M24352 AGCga TgtTaCGgTT TGTtACTGTG ACA...CAAC ACTGgaTGAt ctcAgTGggC gTtcTTA...A AGgtTgAGtA gTGTcCTgCC tGAC — stx₁ X07903 AGCga TgtTaCGgTT TGTtACTGTG ACA...CAAC ACTGgaTGAt ctcAgTGggC gTtcTTA...A AGgtTgAGtA gTGTcCTgCC tGAC — stx₁ Z36899 AGCga TgtTaCGgTT TGTtACTGTG ACA...CAAC ACTGgaTGAt ctcAgTGggC gTtcTTA...A AGgtTgAGtA gTGTcCTgCC tGAC — stx₁ Z36901 AGCga TgtTaCGgTT TGTtACTGTG ACA...CAAC ACTtgaTGAt ctcAgTGggC gTtcTTA...A AGgtTgAGtA gTGTcCTgCC tGAC 1076 stx₂ X61283 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G CGAATCAGCA ATGTGCTTCC GGAG — stx₂ L11079 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G CGAATCAGCA ATGTGCTTCC GGAG — stx₂ M21534 AGCAG TTCTGCGTTT TGTCACTGTC ACA...TGGC ACTGTCTGA. ..AACTGCTC CTGTTTA...G AGAATCAGCA ATGTGCTTCC GGAG — stx₂ M36727 AGCAG TTCTGCGTTT TGTCACTGTC ACA...TGGC ACTGTCTGA. ..AACTGCTC CTGTTTA...G AGAATCAGCA ATGTGCTTCC GGAG — stx₂ U72191 AGCAG TTCTGCGTTT TGTCACTGTC ACA...TGGC ACTGTCTGA. ..AACTGCTC CTGTTTA...G AGAATCAGCA ATGTGCTTCC GGAG — stx₂ X81415 AGCAG TTCTGCGTTT TGTCACTGTC ACA...TGGC ACTGTCTGA. ..AACTGCTC CTGTTTA...G AGAATCAGCA ATGTGCTTCC GGAG — stx₂ X81416 AGCAG TTCTGCGTTT TGTCACTGTC ACA...TGGC ACTGTCTGA. ..AACTGCTC CTGTTTA...G AGAATCAGCA ATGTGCTTCC GGAG — stx₂ X81417 AGCAG TTCTGCGTTT TGTCACTGTC ACA...TGGC ACTGTCTGA. ..AACTGCTC CTGTTTA...G AGAATCAGCA ATGTGCTTCC GGAG — stx₂ X81418 AGCAG TTCTGCGTTT TGTCACTGTC ACA...TGGC ACTGTCTGA. ..AACTGCTC CTGTTTA...G AGAATCAGCA ATGTGCTTCC GGAG — stx₂ E03962 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G CGAATCAGCA ATGTGCTTCC GGAG — stx₂ E03959 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G CGAATCAGCA ATGTGCTTCC GGAG — stx₂ X07865 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G CGAATCAGCA ATGTGCTTCC GGAG — stx₂ Y10775 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G CGAATCAGCA ATGTGCTTCC GGAG — stx₂ Z37725 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G CGAATCAGCA ATGTGCTTCC GGAG 1077 stx₂ Z50754 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G CGAATCAGCA ATGTGCTTCC GGAG — stx₂ X67514 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G CGAATCAGCA ATGTGCTTCC GGAG — stx₂ L11078 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G AGAATCAGCA ATGTGCTTCC GGAG — stx₂ X65949 AGCAG TTCTGCGTTT TGTCACTGTC ACA...AGGC ACTGTCTGA. ..AACTGCTC CTGTGTA...G AGAATCAGCA ATGTGCTTCC GGAG — stx₂ AF043627 AGCAG TTCTGCGTTT TGTCACTGTC ACA...TGGC ACTGTCTGA. ..AACTGCTC CTGTTTA...G AGAATCAGCA ATGTGCTTCC GGAG — Selected sequence for amplification    AG TTCTGCGTTT TGTCACTGTC 1078 primer Selected sequence for hybridization                                      C ACTGTCTGA. ..AACTGCTC CTGT 1085 probe Selected sequence for amplification                                                                            AATCAGCA ATGTGCTTCC G 1079 primer^(a) The sequence numbering refers to the Escherichia coli stx₂ gene fragment (SEQ ID NO. 1077). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. ^(a)This sequence is the reverse-complement of the selected primer.

Annex XXVIII: Strategy for the selection of vanA-specific amplification primers from van sequences. Accession # 926                        952   1230                     1255 SEQ ID NO.: vanA X56895 GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1139 vanA M97297 GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1141 vanA — GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1051 vanA — GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1052 vanA — GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1053 vanA — GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1054 vanA — GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1055 vanA — GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1056 vanA — GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1057 vanA — GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1049 vanA — GTCAAT AGCGCGGACG AATTGGACTA C...GT AGAGGTCTAG CCCGTGTGGA TATG 1050 vanB U94526 GTAAAc gGtaCGGAaG AAcTtaACGC T...GC AGAGGgCTtG CCCGTGTtGA TCTT 1117 vanB U94527 GTAAAc AGtaCGGAaG AAcTaaACGC T...GC AGAGGgCTtG CtCGTGTtGA TCTT — vanB U94528 GTAAAc gGtaCGGAaG AAcTtaACGC T...GC AGAGGgCTtG CCCGTGTtGA TCTT — vanB U94529 GTAAAc gGtaCGGAaG AAcTtaACGC T...GC AGAGGgCTtG CCCGTGTtGA TCTT — vanB U94530 GTAAAc gGtaCGGAaG AAcTtaACGC T...GC AGAGGgCTtG CCCGTGTtGA TCTT — vanB Z83305 GTAAAc gGtaCGGAaG AAcTtaACGC T...GC AGAGGgCTtG CCCGTGTtGA TCTT — vanB U81452 GTAAAc gGtaCGGAaG AAcTtaACGC T...GC AGAGGgCTtG CCCGTGTtGA TCTT — vanB U35369 GTAAAc AGtaCGGAaG AAcTaaACGC T...GC AGAGGgCTtG CtCGTGTtGA TCTT — vanB U72704 GTAAAc gGtaCGGAaG AAcTtaACGC T...GC AGAGGgCTtG CCCGTGTtGA TCTT — vanB L06138 GTAAAc AGtaCGGAaG AAcTaaACGC T...GC AGAGGgCTtG CtCGTGTtGA TCTT — vanB L15304 GTAAAc gGtaCGGAaG AAcTtaACGC T...GC AGAGGgCTtG CCCGTGTtGA TCTT — vanB U00456 GTAAAc AGtaCGGAaG AAcTaaACGC T...GC AGAGGgCTtG CtCGTGTtGA TCTT — vanD AF130997 GTAtgc AagGCaGAaG AAcTGcAgGC A...GC AGAGGatTgG CCCGcaTtGA cCTG — vanE AF136925 GTAgAa caaaaaagtG AtTTatAtAA A...GC AaAGGatTAG CgaGaaTcGA cTTT — Selected sequence for    AAT AGCGCGGACG AATTGGAC 1090 amplification primer Selected sequence for                                     GAGGTCTAG CCCGTGTGGA T 1089 amplification primer^(a) The sequence numbering refers to the Enterococcus faecium vanA gene fragment (SEQ ID NO. 1139). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. ^(a)This sequence is the reverse-complement of the above selected primer.

Annex XXIX: Strategy for the selection of vanB-specific amplification primers from van sequences. Accession # 470                       495   608                       633 SEQ ID NO.: vanA X56895 A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1139 vanA M97297 A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1141 vanA — A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1051 vanA — A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1052 vanA — A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1053 vanA — A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1054 vanA — A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1055 vanA — A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1056 vanA — A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1057 vanA — A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1049 vanA — A CGCaATtGAA tCgGCAaGAC AATAT...ACG GaATCTTtCG tATtCATCAG GAA 1050 vanB U94526 C TGCGATAGAA GCgGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA 1117 vanB U94527 C TGCGATAGAA GCAGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA — vanB U94528 C TGCGATAGAA GCgGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA — vanB U94529 C TGCGATAGAA GCgGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA — vanB U94530 C TGCGATAGAA GCgGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA — vanB Z83305 C TGCGATAGAA GCgGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA — vanB U81452 C TGCGATAGAA GCgGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA — vanB U35369 C TGCGATAGAA GCAGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA — vanB U72704 C TGCGATAGAA GCgGCAGGAC AATAT...ATG GTATCTTCCG CATCCATCAG GAA — vanB L06138 C TGCGATAGAA GCAGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA — vanB L15304 C TGCGATAGAA GCgGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA — vanB U00456 C TGCGATAGAA GCAGCAGGAC AATAT...ACG GTATCTTCCG CATCCATCAG GAA — vanD AF130997 C AGCaATcGAA GaAGCAaGAa AATAT...ACG GctTtTTtaa gATtCATCAG GAA — vanE AF136925 A AGCaATAGAc GaAGCttcAa AATAT...ATG GctTtTTCga CtatgAagAG AAA — Selected sequence for     CGATAGAA GCAGCAGGAC AA 1095 amplification primer Selected sequence for                                     GTATCTTCCG CATCCATCAG 1096 amplification primer^(a) The sequence numbering refers to the Enterococcus faecium vanB gene fragment (SEQ ID NO. 1117). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. ^(a)This sequence is the reverse-complement of the above vanB sequence.

Annex XXX: Strategy for the selection of vanC-specific amplification primers from vanC sequences. Accession # 929                          957   1064                        1092 SEQ ID NO.: vanC1 — GT CGACGGTTTT TTTGATTTTG AAGAGAA...ACGGGTC TGGCTCGAAT CGATTTTTTC GT 1058 vanC1 — GT CGACGGTTTT TTTGATTTTG AAGAGAA...ACGGGTC TGGCTCGAAT CGATTTTTTC GT 1059 vanC1 M75132 GT CGACGGTTTT TTTGATTTTG AAGAGAA...ACGGGTC TGGCTCGAAT CGATTTTTTC GT 1138 vanC2 — GT AGACGGCTTT TTCGATTTTG AAGAAAA...AAAGGTC TTGCTCGCAT CGACTTTTTT GT 1060 vanC2 — GT AGACGGCTTT TTCGATTTTG AAGAAAA...AAAGGTC TTGCTCGCAT CGACTTTTTT GT 1061 vanC2 — GT AGACGGCTTT TTCGATTTTG AAGAAAA...AAAGGTC TTGCTCGCAT CGACTTTTTT GT 1062 vanC2 — GT AGACGGCTTT TTCGATTTTG AAGAAAA...AAAGGTC TTGCTCGCAT CGACTTTTTT GT 1063 vanC2 L29638 GT AGACGGCTTT TTCGATTTTG AAGAAAA...AAAGGTC TTGCTCGCAT CGACTTTTTT GT — vanC2 L29638 GT AGACGGCTTT TTCGATTTTG AAGAAAA...AAAGGTC TTGCTCGCAT CGACTTTTTT GT — vanC3 — GT AGACGGCTTT TTCGATTTTG AAGAAAA...AAAGGTC TTGCTCGCAT CGACTTTTTT GT 1064 vanC3 — GT AGACGGCTTT TTCGATTTTG AAGAAAA...AAAGGTC TTGCTCGCAT CGACTTTTTT GT 1065 vanC3 — GT AGACGGCTTT TTCGATTTTG AAGAAAA...AAAGGaC TTGCTCGCAT CGACTTTTTT GT 1066 vanC3 L29639 GT AGACGGCTTT TTCGATTTTG AAGAAAA...AAAGGTC TTGCTCGCAT CGACTTTTTT GT — Selected sequence     GACGGYTTT TTYGATTTTG AAGA 1101 for resistance primer Selected sequence                                       GGTC TKGCTCGMAT CGAYTTTTT 1102 for resistance primer^(a) The sequence numbering refers to the vanC1 gene fragment (SEQ ID NO. 1138). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequence displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)This sequence is the reverse-complement of the selected sequence.

Annex XXXI: Strategy for the selection of Streptococcus pneumoniae-specific amplification primers and hybridization probes from pbp1a sequences. SEQ ID Accession # 453                                                     505   678                          706 NO.: pbp1a M90528 A TTGACTAcCC AAGCATaCAc TATGCtAAtG CtATTTCAAG TAATACAACC GA...TATATG ATGACaGAtA TGATGAAAAC CGT... — pbp1a X67873 A TCGACTAcCC AAGtATtCAc TActCAAAtG CCATTTCAAG TAAcACAACC GA...TATATG ATGACCGAAA TGATGAAAAC AGT... — pbp1a AB006868 A TCGACTAcCC AAGtATtCAc TActCAAAtG CCATTTCAAG TAAcACAACC GA...TATATG ATGACCGACA TGATGAAAAC AGT... — pbp1a AF046234 A TCGACTAcCC AAGtATtCAc TActCAAAtG CCATTTCAAG TAAcACAACC GA...TATATG ATGACCGAAA TGATGAAAAC TGT... — pbp1a A TCGACTAcCC AAGtATtCAc TActCAAAtG CCATTTCAAG TAAcACAACC GA...TATATG ATGACCGACA TGATGAAAAC TGT... 1014 pbp1a A TCGACTAcCC AAGtATtCAc TActCAAAtG CCATTTCAAG TAAcACAACC GA...TACATG ATGACCGAAA TGATGAAAAC TGT... 1017 pbp1a AB006873 A TCGACTAcCC AAGtcTtCAc TActCAAAtG CCATTTCAAG TAAcACAACC GA...TATATG ATGACCGACA TGATGAAAAC AGT... — pbp1a AF139883 A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TATATG ATGACCGACA TGATGAAAAC AGT... 1169 pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TATATG ATGACCGACA TGATGAAAAC AGT... 1004 pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TATATG ATGACCGACA TGATGAAAAC AGT... 1007 pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TATATG ATGACCGACA TGATGAAAAC AGT... 1008 pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TATATG ATGACCGACA TGATGAAAAC AGT... 1009 pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TATATG ATGACCGACA TGATGAAAAC AGT... 1011 pbp1a AF159448 A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TATATG ATGACCGACA TGATGAAAAC AGT... — pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TACATG ATGACCGAAA TGATGAAAAC TGT... 1005 pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TACATG ATGACCGAAA TGATGAAAAC TGT... 1015 pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TACATG ATGACCGAAA TGATGAAAAC TGT... 1006 pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TACATG ATGACCGAAA TGATGAAAAC TGT... 1012 pbp1a X67867 A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAATACAACA GA...TACATG ATGACCGAAA TGATGAAAAC TGT... — pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAAcACAACT GA...TATATG ATGACtGAAA TGATGAAAAC TGT... 1010 pbp1a Z49094 A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAAcACAACT GA...TATATG ATGACtGAAA TGATGAAAAC TGT... — pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAAcACAACT GA...TATATG ATGACtGAAA TGATGAAAAC TGT... 1013 pbp1a A TCGACTATCC AAGCATGCAT TATGCAAACG CCATTTCAAG TAAcACAACT GA...TATATG ATGACtGAAA TGATGAAAAC TGT... 1016 pbp1a X67870 A TCGACTATCC AAGtATGCAT TAcGCAAACG CCATTTCAAG TAAcACAACT GA...TATATG ATGACCGAAA TGATGAAAAC TGT... — pbp1a A TTGACTATCC AAGtATtCAc TActCAAAtG CtATTTCAAG TAATACAACT GA...TATATG ATGACtGAAA TGATGAAAAC TGT... 1018 pbp1a AJ002290 A TTGAtTAcCC AActATGgtc TATGCtAACG CtATTTCAAG TAATACAACT GA...TACATG ATGACtGAAA TGATGAAAAC AGT... — pbp1a X67871 A TCGACTAcCC AAGtcTtCAc TActCAAAtG CCATTTCAAG TAAcACAACC GA...TACATG ATGACaGAAA TGATGAAAAC AGT... — Selected sequences for amplification primers     GACTATCC AAGCATGCAT TATG 1130                                                                  ATG ATGACHGAMA TGATGAAAAC 1129 Selected sequence for hybridization probe                             CAAACG CCATTTCAAG TAATACAAC 1197 The sequence numbering refers to the Streptococcus pneumoniae pbp1a gene fragment (SEQ ID NO. 1004). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dotes indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “H” stands for A, C or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. SEQ ID Accession #    756                        783   813                         840 SEQ ID NO.: pbp1a M90528 ...GCTGGTAA aACtGGTACg TCTaACTATA...A ATACgGGTTA TGTAGCTCCG GAcGAAA — pbp1a X67873 ...GCTGGTAA aACAGGaACc TCTAACTATA...A CCtCTcaaTt TGTAGCaCCt GATGAAC — pbp1a AB006868 ...GCTGGTAA aACAGGaACc TCTAACTATA...A CCtCTcaaTt TGTAGCaCCt GAcGAAC — pbp1a AF046234 ...GCAGGTAA aACAGGTACT TCTAACTATA...A ACACTGGTTA CGTAGCTCCA GATGAAA — pbp1a ...GCAGGTAA aACAGGTACT TCTAACTATA...A ACACTGGTTA CGTAGCTCCA GATGAAA 1014 pbp1a ...GCTGGTAA GACAGGTACT TCTAACTACA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1017 pbp1a AB006873 ...GCAGGTAA GACAGGTACT TCTAACTATA...A ACACTGGCTA CGTAGCTCCA GATGAAA — pbp1a AF139883 ...GCTGGTAA aACAGGaACc TCTAACTATA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1169 pbp1a ...GCTGGTAA aACAGGaACc TCTAACTATA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1004 pbp1a ...GCTGGTAA aACAGGaACc TCTAACTATA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1007 pbp1a ...GCTGGTAA aACAGGaACc TCTAACTATA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1008 pbp1a ...GCTGGTAA aACAGGaACc TCTAACTATA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1009 pbp1a ...GCTGGTAA aACAGGaACc TCTAACTATA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1011 pbp1a AF159448 ...GCTGGTAA aACAGGaACc TCTAACTATA...A ACACTGGCTA TGTAGCTCCA GATGAAA — pbp1a ...GCTGGTAA GACAGGTACT TCTAACTACA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1005 pbp1a ...GCTGGTAA GACAGGTACT TCTAACTACA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1015 pbp1a ...GCTGGTAA GACAGGTACT TCTAACTACA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1006 pbp1a ...GCTGGTAA GACAGGTACT TCTAACTACA...A ACACTGGCTA TGTAGCTCCA GATGAAA 1012 pbp1a X67867 ...GCTGGTAA GACAGGTACT TCTAACTACA...A ACACTGGCTA TGTAGCTCCA GATGAAA — pbp1a ...GCAGGTAA GACAGGTACT TCTAACTATA...A ACACTGGTTA CGTAGCTCCA GATGAAA 1010 pbp1a Z49094 ...GCAGGTAA GACAGGTACT TCTAACTATA...A ACACTGGTTA CGTAGCTCCA GATGAAA — pbp1a ...GCAGGTAA GACAGGTACT TCTAACTATA...A ACACTGGCTA CGTAGCTCCA GATGAAA 1013 pbp1a ...GCAGGTAA GACAGGTACT TCTAACTATA...A ACACTGGCTA CGTAGCTCCA GATGAAA 1016 pbp1a X67870 ...GCAGGTAA GACAGGTACT TCTAACTATA...A ACACTGGCTA CGTAGCTCCA GATGAAA — pbp1a ...GCAGGTAA GACAGGTACT TCTAACTATA...A ACACTGGCTA CGTAGCTCCA GATGAAA 1018 pbp1a AJ002290 ...GCAGGTAA GACgGGTACa TCTAACTACA...A ACACTGGCTA C~~~~~~~~~ ~~~~~~~ — pbp1a X67871 ...GCTGGTAA aACAGGTACc TCTAACTATA...A ACACTGGTTA CGTAGCTCCA GATGAAA — Selected sequence for hybridization probe       GGTAA GACAGGTACT TCTAACT 1193 Selected sequence for amplification primer^(a)                                         ACTGGYTA YGTAGCTCCA GATG 1131 The sequence numbering refers to the Streptococcus pneumoniae pbp1a gene fragment (SEQ ID NO. 1004). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. “~” indicates incomplete sequence data. “R” “Y” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. ^(a)This sequence is the reverse-complement of the selected primer.

Annex XXXII: Specific and ubiquitous primers for nucleic acid amplification (toxin sequences). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Toxin gene: cdtA 2123 5′-TCT ACC ACT GAA GCA TTA C 2129^(a) 442-460 2124^(b) 5′-TAG GTA CTG TAG GTT TAT TG 2129^(a) 580-599 Toxin gene: cdtB 2126 5′-ATA TCA GAG ACT GAT GAG 2130^(a) 2665-2682 2127^(b) 5′-TAG CAT ATT CAG AGA ATA TTG T 2130^(a) 2746-2767 Toxin gene: stx₁ 1081 5′-ATG TCA GAG GGA TAG ATC CA 1076^(a) 233-252 1080^(b) 5′-TAT AGC TAC TGT CAC CAG ACA ATG T 1076^(a) 394-418 Toxin gene: stx₂ 1078 5′-AGT TCT GCG TTT TGT CAC TGT C 1077^(a) 546-567 1079^(b) 5′-CGG AAG CAC ATT GCT GAT T 1077^(a) 687-705 Toxin genes: stx₁, and stx₂ 1082 5′-TTG ARC RAA ATA ATT TAT ATG TG 1076^(a) 278-300 1083^(b) 5′-TGA TGA TGR CAA TTC AGT AT 1076^(a) 781-800 ^(a)Sequences from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Annex XXXIII: Molecular beacon internal hybridization probes for specific detection of toxin sequences. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence^(a) NO. position Toxin gene: cdtA 2125^(b) 5′-CAC GCG GAT TTT GAA TCT CTT CCT CTA 2129^(c) 462-488 GTA GCG CGT G Toxin gene: cdtB 2128 5′-CAA CGC TGG AGA ATC TAT ATT TGT AGA 2130^(c) 2714-2740 AAC TGC GTT G Toxin gene: stx₁ 1084 5′-CCA CGC CGC TTT GCT GAT TTT TCA CAT 1076^(c) 337-363 GTT ACC GCG TGG 2012^(d) 5′-CCG CGG ATT ATT AAA CCG CCC TTC CGC 1076^(c) 248-264 GG-MR-HEG-ATG TCA GAG GGA TAG ATC CA Toxin gene: stx₂ 1085 5′-CCA CGC CAC TGT CTG AAA CTG CTC CTG 1077^(c) 617-638 TG CGT GG ^(a)Underlined nucleotides indicate the molecular beacon's stem. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(c)Sequences from databases. ^(d)Scorpion primer.

Annex XXXIV: Specific and ubiquitous primers for nucleic acid amplification (van sequences). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Resistance gene: vanA 1086 5′-CTA CTC CCG CCT TTT GGG TT 1049-1057^(a) 513-532^(b) 1087^(c) 5′-CTC ACA GCC CGA AAC AGC CT 1049-1057^(a) 699-718^(b) 1086 5′-CTA CTC CCG CCT TTT GGG TT 1049-1057^(a) 513-532^(b) 1088^(c) 5′-TGC CGT TTC CTG TAT CCG TC 1049-1057^(a) 885-904^(b) 1086 5′-CTA CTC CCG CCT TTT GGG TT 1049-1057^(a) 513-532^(b) 1089^(c) 5′-ATC CAC ACG GGC TAG ACC TC 1049-1057^(a) 933-952^(b) 1090 5′-AAT AGC GCG GAC GAA TTG GAC 1049-1057^(a) 629-649^(b) 1091^(c) 5′-AAC GCG GCA CTG TTT CCC AA 1049-1057^(a) 734-753^(b) 1090 5′-AAT AGC GCG GAC GAA TTG GAC 1049-1057^(a) 629-649^(b) 1089^(c) 5′-ATC CAC ACG GGC TAG ACC TC 1049-1057^(a) 933-952^(b) 1092 5′-TCG GCA AGA CAA TAT GAC AGC 1049-1057^(a) 662-682^(b) 1088^(c) 5′-TGC CGT TTC CTG TAT CCG TC 1049-1057^(a) 885-904^(b) Resistance gene: vanB 1095 5′-CGA TAG AAG CAG CAG GAC AA 1117^(d) 473-492  1096^(c) 5′-CTG ATG GAT GCG GAA GAT AC 1117^(d) 611-630  Resistance genes: vanA, vanB 1112 5′-GGC TGY GAT ATT CAA AGC TC 1049-1057, 1117^(a) 437-456^(b) 1113^(c) 5′-ACC GAC CTC ACA GCC CGA AA 1049-1057, 1117^(a) 705-724^(b) 1112 5′-GGC TGY GAT ATT CAA AGC TC 1049-1057, 1117^(a) 437-456^(b) 1114^(c) 5′-TCW GAG CCT TTT TCC GGC TCG 1049-1057, 1117^(a) 817-837^(b) 1115 5′-TTT CGG GCT GTG AGG TCG GBT GHG CG 1049-1057, 1117^(a) 705-730^(b) 1114^(c) 5′-TCW GAG CCT TTT TCC GGC TCG 1049-1057, 1117^(a) 817-837^(b) 1116 5′-TTT CGG GCT GTG AGG TCG GBT GHG CGG 1049-1057, 1117^(a) 705-731^(b) 1114^(c) 5′-TCW GAG CCT TTT TCC GGC TCG 1049-1057, 1117^(a) 817-837^(b) 1112 5′-GGC TGY GAT ATT CAA AGC TC 1049-1057, 1117^(a) 437-456^(b) 1118^(c) 5′-TTT TCW GAG CCT TTT TCC GGC TCG 1049-1057, 1117^(a) 817-840^(b) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the vanA sequence fragment (SEQ ID NO. 1051). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)Sequences from databases. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position 1115 5′-TTT CGG GCT GTG AGG TCG GBT GHG CG 1049-1057, 1117^(a) 705-730^(b) 1118^(c) 5′-TTT TCW GAG CCT TTT TCC GGC TCG 1049-1057, 1117^(a) 817-840^(b) 1116 5′-TTT CGG GCT GTG AGG TCG GBT GHG CGG 1049-1057, 1117^(a) 705-731^(b) 1118^(c) 5′-TTT TCW GAG CCT TTT TCC GGC TCG 1049-1057, 1117^(a) 817-840^(b) 1119 5′-TTT CGG GCT GTG AGG TCG GBT GHG C 1049-1057, 1117^(a) 705-729^(b) 1118^(c) 5′-TTT TCW GAG CCT TTT TCC GGC TCG 1049-1057, 1117^(a) 817-840^(b) 1120 5′-TTT CGG GCT GTG AGG TCG GBT GHG 1049-1057, 1117^(a) 705-728^(b) 1118^(c) 5′-TTT TCW GAG CCT TTT TCC GGC TCG 1049-1057, 1117^(a) 817-840^(b) 1121 5′-TGT TTG WAT TGT CYG GYA TCC C 1049-1057, 1117^(a) 408-429^(b) 1111^(c) 5′-CTT TTT CCG GCT CGW YTT CCT GAT G 1049-1057, 1117^(a) 806-830^(b) 1112 5′-GGC TGY GAT ATT CAA AGC TC 1049-1057, 1117^(a) 437-456^(b) 1111^(c) 5′-CTT TTT CCG GCT CGW YTT CCT GAT G 1049-1057, 1117^(a) 806-830^(b) 1123 5′-TTT CGG GCT GTG AGG TCG GBT G 1049-1057, 1117^(a) 705-726^(b) 1111^(c) 5′-CTT TTT CCG GCT CGW YTT CCT GAT G 1049-1057, 1117^(a) 806-830^(b) 1112 5′-GGC TGY GAT ATT CAA AGC TC 1049-1057, 1117^(a) 437-456^(b) 1124^(c) 5′-GAT TTG RTC CAC YTC GCC RAC A 1049-1057, 1117^(a) 757-778^(b) Resistance gene: vanC1 1103 5′-ATC CCG CTA TGA AAA CGA TC 1058-1059^(a) 519-538^(d) 1104^(c) 5′-GGA TCA ACA CAG TAG AAC CG 1058-1059^(a) 678-697^(d) Resistance genes: vanC1, vanC2, vanC3 1097 5′-TCY TCA AAA GGG ATC ACW AAA GTM AC 1058-1066^(a) 607-632^(d) 1098^(c) 5′-TCT TCA AAA TCG AAA AAG CCG TC 1058-1066^(a) 787-809^(d) 1099 5′-TCA AAA GGG ATC ACW AAA GTM AC 1058-1066^(a) 610-632^(d) 1100^(c) 5′-GTA AAK CCC GGC ATR GTR TTG ATT TC 1058-1066^(a) 976-1001^(d) 1101 5′-GAC GGY TTT TTY GAT TTT GAA GA 1058-1066^(a) 787-809^(d) 1102^(c) 5′-AAA AAR TCG ATK CGA GCM AGA CC 1058-1066^(a) 922-944^(d) Resistance genes: vanC2, vanC3 1105 5′-CTC CTA CGA TTC TCT TGA YAA ATC A 1060-1066, 1140^(a) 487-511^(e) 1106^(c) 5′-CAA CCG ATC TCA ACA CCG GCA AT 1060-1066, 1140^(a) 690-712^(e) ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the vanA sequence fragment (SEQ ID NO. 1051). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)The nucleotide positions refer to the vanC1 sequence fragment (SEQ ID NO. 1058). ^(e)The nucleotide positions refer to the vanC2 sequence fragment (SEQ ID NO. 1140). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Resistance gene: vanD 1591 5′-ATG AGG TAA TAG AAC GGA TT 1594 797-837  1592^(b) 5′-CAG TAT TTC AGT AAG CGT AAA 1594 979-999  Resistance gene: vanE 1595 5′-AAA TAA TGC TCC ATC AAT TTG CTG A 1599^(a) 74-98  1596^(b) 5′-ATA GTC GAA AAA GCC ATC CAC AAG 1599^(a) 394-417  1597 5′-GAT GAA TTT GCG AAA ATA CAT GGA 1599^(a) 163-186  1598^(b) 5′-CAG CCA ATT TCT ACC CCT TTC AC 1599^(a) 319-341  Sequencing primers (vanAB) 1112 5′-GGC TGY GAT ATT CAA AGC TC 1139^(a) 737-756  1111^(b) 5′-CTT TTT CCG GCT CGW YTT CCT GAT G 1139^(a) 1106-1130  Sequencing primers (vanA, vanX, vanY) 1150 5′-TGA TAA TCA CAC CGC ATA CG 1141^(a) 860-879  1151^(b) 5′-TGC TGT CAT ATT GTC TTG CC 1141^(a) 1549-1568  1152 5′-ATA AAG ATG ATA GGC CGG TG 1141^(a) 1422-1441  1153^(b) 5′-CTC GTA TGT CCC TAC AAT GC 1141^(a) 2114-2133  1154 5′-GTT TGA AGC ATA TAG CCT CG 1141^(a) 2520-2539  1155^(b) 5′-CAG TGC TTC ATT AAC GTA GTC 1141^(a) 3089-3109  Sequencing primers (vanC1) 1110 5′-ACG AGA AAG ACA ACA GGA AGA CC 1138^(a) 122-144  1109^(b) 5′-ACA TCG TGA TCG CTA AAA GGA GC 1138^(a) 1315-1337  Sequencing primers (vanC2, vanC3) 1108 5′-GTA AGA ATC GGA AAA GCG GAA GG 1140^(a) 1-23 1107^(b) 5′-CTC ATT TGA CTT CCT CCT TTG CT 1140^(a) 1064-1086  ^(a)Sequences from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Annex XXXV: Internal hybridization probes for specific detection of van sequences. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Resistance gene: vanA 1170 5′-ACG AAT TGG ACT ACG CAA TT 1049-1057^(a)  639-658^(b) 2292 5′-GAA TCG GCA AGA CAA TAT G 2293^(c) 583-601 Resistance gene: vanB 1171 5′-ACG AGG ATG ATT TGA TTG TC 1117^(c) 560-579 2294 5′-AAA CGA GGA TGA TTT GAT TG 2296^(a) 660-679 2295 5′-TTG AGC AAG CGA TTT CGG 2296^(a) 614-631 Resistance gene: vanD 2297 5′-TTC AGG AGG GGG ATC GC 1594^(c) 458-474 ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the vanA sequence fragment (SEQ ID NO. 1051). ^(c)Sequences from databases.

Annex XXXVI: Specific and ubiquitous primers for nucleic acid amplification (pbp sequences). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Resistance gene: pbp1a 1129 5′-ATG ATG ACH GAM ATG ATG AAA AC 1004-1018^(a)  681-703^(b) 1131^(c) 5′-CAT CTG GAG CTA CRT ARC CAG T 1004-1018^(a)  816-837^(b) 1130 5′-GAC TAT CCA AGC ATG CAT TAT G 1004-1018^(a)  456-477^(b) 1131 5′-CAT CTG GAG CTA CRT ARC CAG T 1004-1018^(a)  816-837^(b) 2015 5′-CCA AGA AGC TCA AAA ACA TCT G 2047^(d) 909-930 2016^(c) 5′-TAD CCT GTC CAW ACA GCC AT 2047^(d) 1777-1796 Sequencing primers (pbp1a) 1125 5′-ACT CAC AAC TGG GAT GGA TG 1169^(d) 873-892 1126^(c) 5′-TTA TGG TTG TGC TGG TTG AGG 1169^(d) 2140-2160 1125 5′-ACT CAC AAC TGG GAT GGA TG 1169^(d) 873-892 1128^(c) 5′-GAC GAC YTT ATK GAT ATA CA 1169^(d) 1499-1518 1127 5′-KCA AAY GCC ATT TCA AGT AA 1169^(d) 1384-1403 1126^(c) 5′-TTA TGG TTG TGC TGG TTG AGG 1169^(d) 2140-2160 Sequencing primers (pbp2b) 1142 5′-GAT CCT CTA AAT GAT TCT CAG GTG G 1172^(d)  1-25 1143^(c) 5′-CAA TTA GCT TAG CAA TAG GTG TTG G 1172^(d) 1481-1505 1142 5′-GAT CCT CTA AAT GAT TCT CAG GTG G 1172^(d)  1-25 1145^(c) 5′-AAC ATA TTK GGT TGA TAG GT 1172^(d) 793-812 1144 5′-TGT YTT CCA AGG TTC AGC TC 1172^(d) 657-676 1143^(c) 5′-CAA TTA GCT TAG CAA TAG GTG TTG G 1172^(d) 1481-1505 Sequencing primers (pbp2x) 1146 5′-GGG ATT ACC TAT GCC AAT ATG AT 1173^(d) 219-241 1147^(c) 5′-AGC TGT GTT AGC VCG AAC ATC TTG 1173^(d) 1938-1961 1146 5′-GGG ATT ACC TAT GCC AAT ATG AT 1173^(d) 219-241 1149^(c) 5′-TCC YAC WAT TTC TTT TTG WG 1173^(d) 1231-1250 1148 5′-GAC TTT GTT TGG CGT GAT AT 1173^(d) 711-730 1147^(c) 5′-AGC TGT GTT AGC VCG AAC ATC TTG 1173^(d) 1938-1961 ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the pbp1a sequence fragment (SEQ ID NO. 1004). ^(c)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(d)Sequences from databases.

Annex XXXVII: Internal hybridization probes for specific detection of pbp sequences. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Resistance gene: pbp1a 1132 5′-AGT GAA AAR ATG GCT GCT GC 1004-1018^(a)  531-550^(b) 1133 5′-CAT CAA GAA CAC TGG CTA YGT AG 1004-1018^(a)  806-828^(b) 1134 5′-CTA GAT AGA GCT AAA ACC TTC CT 1004-1018^(a)  417-439^(b) 1135 5′-CAT TAT GCA AAC GCC ATT TCA AG 1004-1018^(a)  471-493^(b) 1192 5′-GGT AAA ACA GGA ACC TCT AAC T 1004-1018^(a)  759-780^(b) 1193 5′-GGT AAG ACA GGT ACT TCT AAC T 1004-1018^(a)  759-780^(b) 1194 5′-CAT TTC AAG TAA TAC AAC AGA ATC 1004-1018^(a)  485-508^(b) 1195 5′-CAT TTC AAG TAA CAC AAC TGA ATC 1004-1018^(a)  485-508^(b) 1196 5′-GCC ATT TCA AGT AAT ACA ACA GAA 1004-1018^(a)  483-506^(b) 1197 5′-CAA ACG CCA TTT CAA GTA ATA CAA C 1004-1018^(a)  478-502^(b) 1094 5′-GGT AAA ACA GGT ACT TCT AAC TA 1004-1018^(a)  759-781^(b) 1214 5′-GGT AAA ACA GGT ACC TCT AAC TA 1004-1018^(a)  759-781^(b) 1216 5′-GGT AAG ACT GGT ACA TCA AAC TA 1004-1018^(a)  759-781^(b) 1217 5′-CAA ATG CCA TTT CAA GTA ACA CAA C 1004-1018^(a)  478-502^(b) 1218 5′-CAA ACG CCA TTT CAA GTA ACA CAA C 1004-1018^(a)  478-502^(b) 1219 5′-CAA ATG CTA TTT CAA GTA ATA CAA C 1004-1018^(a)  478-502^(b) 1220 5′-CAA ACG CCA TTT CAA GTA ATA CGA C 1004-1018^(a)  478-502^(b) 2017 5′-ACT TTG AAT AAG GTC GGT CTA G 2047^(c) 1306-1327 2018 5′-ACA CTA AAC AAG GTT GGT TTA G 2063 354-375 2019 5′-ACA CTA AAC AAG GTC GGT CTA G 2064 346-367 2020 5′-GTA GCT CCA GAT GAA ATG TTT G 2140^(c) 1732-1753 2021 5′-GTA GCT CCA GAC GAA ATG TTT G 2057 831-852 2022 5′-GTA GCT CCA GAT GAA ACG TTT G 2053^(c) 805-826 2023 5′-GTA ACT CCA GAT GAA ATG TTT G 2056 819-840 2024 5′-AGT GAA AAG ATG GCT GCT GC 2048^(c) 1438-1457 2025 5′-AGT GAG AAA ATG GCT GCT GC 2047^(c) 1438-1457 2026 5′-TCC AAG CAT GCA TTA TGC AAA CG 2047^(c) 1368-1390 2027 5′-TCG GTC TAG ATA GAG CTA AAA CG 2047^(c) 1319-1341 2028 5′-TAT GCT CTT CAA CAA TCA CG 2047^(c) 1267-1286 2029 5′-AGC CGT TGA GAC TTT GAA TAA G 2047^(c) 1296-1317 2030 5′-CTT AAT GGT CTT GGT ATC G 2047^(c) 1345-1366 2031 5′-CGT GAC TGG GGT TCT GCT ATG A 2049^(c) 1096-1117 2032 5′-CGT GAC TGG GGA TCA TCA ATG A 2047^(c) 1096-1117 2033 5′-CGT GAC TGG GGT TCT GCC ATG A 2057 195-216 2034 5′-ATC AAG AAC ACT GGC TAT GTA G 2050^(c) 787-808 2035 5′-ATC AAG AAC ACT GGC TAC GTA G 2051^(c) 787-808 2036 5′-ATC AAG AAC ACT GGT TAC GTA G 2047 1714-1735 2037 5′-ATC AAA AAT ACT GGT TAT GTA G 2057 813-834 2038 5′-ATC AAG AAT ACT GGC TAC GTA G 2052^(c) 757-778 2039 5′-ATC AAA AAC ACT GGC TAT GTA G 2053^(c) 787-808 ^(a)These sequences were aligned to derive the corresponding primer. ^(b)The nucleotide positions refer to the pbp1a sequence fragment (SEQ ID NO. 1004). ^(c)Sequence from databases.

Annex XXXVIII: Strategy for the selection of vanAB-specific amplification primers and vanA- and vanB-specific hybridization probes from van sequences. SEQ ID Accession # 734                      759   936                      961 NO.: vanA X56895 GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1139 vanA M97297 GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1141 vanA GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1051 vanA GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1052 vanA GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1053 vanA GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1054 vanA GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1055 vanA GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1056 vanA GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1057 vanA GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1049 vanA GTAGGCT GCGATATTCA AAGCTCAGC...CGGAACGAATT GGACTACGCA ATTGAA... 1050 vanB U94526 GTGGGCT GTGATATTCA AAGCTCCGC...CGGAaGAAcT taACgctGCg ATaGAA... 1117 vanB U94527 GTAGGCT GCGATATTCA AAGCTCCGC...CGGAaGAAcT aaACgctGCg ATaGAA... — vanB U94528 GTGGGCT GTGATATTCA AAGCTCCGC...CGGAaGAAcT taACgctGCg ATaGAA... — vanB U94529 GTGGGCT GTGATATTCA AAGCTCCGC...CGGAaGAAcT taACgctGCg ATaGAA... — vanB U94530 GTGGGCT GTGATATTCA AAGCTCCGC...CGGAaGAAcT taACgctGCg ATaGAA... — vanB Z83305 GTGGGCT GTGATATTCA AAGCTCCGC...CGGAaGAAcT taACgctGCg ATaGAA... — vanB U81452 GTGGGCT GTGATATTCA AAGCTCCGC...CGGAaGAAcT taACgctGCg ATaGAA... — vanB U35369 GTAGGCT GCGATATTCA AAGCTCCGC...CGGAaGAAcT aaACgctGCg ATaGAA... — vanB U72704 GTGGGCT GCGATATTCA AAGCTCCGC...CGGAaGAAcT taACgctGCg ATaGAA... — vanB L06138 GTAGGCT GCGATATTCA AAGCTCCGC...CGGAaGAAcT aaACgctGCg ATaGAA... — vanB L15304 GTGGGCT GTGATATTCA AAGCTCCGC...CGGAaGAAcT taACgctGCg ATaGAA... — vanB U00456 GTAGGCT GCGATATTCA AAGCTCCGC...CGGAaGAAcT aaACgctGCg ATaGAA... — vanD AF130997 GTGGGaT GCGATATTCA AAGCTCCGT...CAGAaGAAcT GcAggcaGCA ATcGAA... — vanE AF136925 GTAGGtT GTGgTATcgg AgctgCAGC...AAAgtGAtTT atAtaAaGCA ATaGAC... — Selected sequence    GGCT GYGATATTCA AAGCTC 1112 for amplification primer Selected sequence                                   ACGAATT GGACTACGCA ATT (vanA) 1170 for hybridization probe The sequence numbering refers to the Enterococcus faecium vanA gene fragment (SEQ ID NO. 1139). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. “R” “Y” “M” “K” “W” and “S” designate nucleotide positions which are degenerated. “R” stands for A or G; “Y” stands for C or T; “M” stands for A or C; “K” stands for G or T; “W” stands for A or T; “S” stands for C or G. “I” stands for inosine which is a nucleotide analog that can bind to any of the four nucleotides A, C, G or T. SEQ ID Accession # 1038                    1063   1103                          1133 NO.: vanA X56895 GAAACagt GccGcGTTag TTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1139 vanA M97297 GAAACagt GccGcgTTag TTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1141 vanA GAAACagt GccGcgTTag TTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1051 vanA GAAACagt GccGcgTTag cTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1052 vanA GAAACagt GccGcgTTag cTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1053 vanA GAAACagt GccGcgTTag TTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1054 vanA GAAACagt GccGcgTTag cTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1055 vanA GAAACagt GccGcgTTag cTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1056 vanA GAAACagt GccGcgTTag cTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1057 vanA GAAACagt GccGcgTTag cTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1049 vanA GAAACagt GccGcgTTag cTGTtGGC...ATT CATCAGGAAG TCGAGCCGGA AAAAGGCT 1050 vanB U94526 GGAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT 1117 vanB U94527 GAAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT — vanB U94528 GGAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT — vanB U94529 GGAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT — vanB U94530 GGAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT — vanB Z83305 GGAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT — vanB U81452 GGAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT — vanB U35369 GAAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT — vanB U72704 GGAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGAT — vanB L06138 GAAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT — vanB L15304 GGAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT — vanB U00456 GAAACGAG GATGATTTGA TTGTCGGC...ATC CATCAGGAAA ACGAGCCGGA AAAAGGCT — vanD AF130997 GAAACGga aATGATcTcA TgGctGGC...ATT CATCAGGAAG cacAGCCGGA aAAGGGAT — vanE AF136925 GGAA...t G AacAaTTGg TcGTtGGA...TAT gAagAGaAAt ACaA...... ......TT — Selected sequence    ACGAG GATGATTTGA TTGTC (vanB) 1171 for hybridization probe Selected sequence                                    CATCAGGAAR WCGAGCCGGA AAAAG 1111 for amplification prime^(a) The sequence numbering refers to the Enterococcus faecium vanA gene fragment (SEQ ID NO. 1139). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. “R” and “W” designate nucleotide positions which are degenerated. “R” stands for A or G; “W” stands for A or T ^(a)This sequence is the reverse-complement of the above selected primer.

Annex XXXIX: Internal hybridization probe for specific detection of mecA. Originating DNA fragment SEQ ID SEQ ID Nucleotide NO. Nucleotide sequence NO. position Resistance gene: mecA 1177 5′-GCT CAA CAA GTT CCA 1178^(a) 1313-1332 GAT TA ^(a)Sequence from databases.

Annex XL: Specific and ubiquitous primers for nucleic acid amplification (hexA sequences). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Bacterial species: Streptococcus pneumoniae 1179 5′-ATT TGG TGA CGG GTG ACT TT 1183^(a) 431-450 1181^(b) 5′-AGC AGC TTA CTA GAT GCC GT 1183-1191^(c)  652-671^(d) Sequencing primers 1179 5′-ATT TGG TGA CGG GTG ACT TT 1183^(a) 431-450 1182^(b) 5′-AAC TGC AAG AGA TCC TTT GG 1183^(a) 1045-1064 ^(a)Sequences from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(c)These sequences were aligned to derive the corresponding primer. ^(d)The nucleotide positions refer to the hexA sequence fragment (SEQ ID NO. 1183).

Annex XLI: Internal hybridization probe for specific detection of hexA sequences. Originating DNA fragment SEQ SEQ ID Nucleotide ID NO. Nucleotide sequence NO. position Bacterial species: Streptococcus pneumoniae 1180^(a) 5′-TCC ACC GTT GCC 1183-1191^(b) 629-647^(c) AAT CGC A ^(a)This sequences is from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(b)These sequences were aligned to derive the corresponding primer. ^(c)The nucleotide positions refer to the hexA sequence fragment (SEQ ID NO. 1183).

Annex XLII: Strategy for the selection of Streptococcus pneumoniae species-specific amplification primers and hybridization probe from hexA sequences. 428                       453   626                       S. pneumoniae TGG ATTTGGTGAC GGGTGACTTT TAT...ATTTG CGATTGGCAA CGGTGGAGCA S. pneumoniae ~~~ ~~~~~~TGAC GGGTGACTTT TAT...ATTTG CGATTGGCAA CGGTGGAGCA S. pneumoniae ~~~ ~~~~~~TGAC GGGTGACTTT TAT...ATTTG CGATTGGCAA CGGTGGAGCA S. pneumoniae ~~~ ~~~~~~TGAC GGGTGACTTT TAT...ATTTG CGATTGGCAA CGGTGGAGCA S. pneumoniae ~~~ ~~~~~~TGAC GGGTGACTTT TAT...ATTTG CGATTGGCAA CGGTGGAGCA S. oralis ~~~ ~~~~~~~~~~GGGTGACTTT TAT...ATCca CGAcTGGCAg CtGTGGAGCA S. mitis ~~~ ~~~~GGTGAC GGGTGACTTT TAT...ATTca CGATTGGCAg CtGTGGAGCA S. mitis ~~~ ~~~~~~TGAC GGGTGACTTT CAG...GCGaG gagcTGtCtc CtaTGGAGCG S. mitis ~~~ ~~~~~~TGAC GGGTGACTTT CAG...GCGaG gaAcTGtCtc CtaTGGAGCG Selected sequence for     ATTTGGTGAC GGGTGACTTT amplification primer Selected sequences for                                                             amplification primers^(a)                                                                 Selected sequence for                                    TG CGATTGGCAA CGGTGGA hybridization probe^(a) SEQ ID                           674   1042                    1067 NO.: S. pneumoniae AACGGCATCT AGTAAGCTGC TCCA...AATCCAAAG GATCTCTTGC AGTTGGC 1183 S. pneumoniae AACGGCATCT AGTAAGCTGC TCCA...AATCCAAAG GATCTCTTG~ ~~~~~~~ 1184 S. pneumoniae AACGGCATCT AGTAAGCTGC TCCA...AATCCAAAG GATCTCT~~~ ~~~~~~~ 1185 S. pneumoniae AACGGCATCT AGTAAGCTGC TCCA...AATCCAAAG GATCTCTT~~ ~~~~~~~ 1186 S. pneumoniae AACGGCATCT AGTAAGCTGC TCCG...AATCCAAAG GATCTCTT~~ ~~~~~~~ 1187 S. oralis AgCGGCAgCT AGTAAGCTcC TCCA...~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ 1188 S. mitis AgCGGCATCT AGTAAaCTGC TTCA...AATCCAAAG GATCTCTT~~ ~~~~~~~ 1189 S. mitis TcaGGCAgCa gGgAAaCTGC TGGA...~~~~~~~~~ ~~~~~~~~~~ ~~~~~~~ 1190 S. mitis TcaGGCAgCg gGgAAatTGC TAGA...AATCCAAAG GATCTCTT~~ ~~~~~~~ 1191 Selected sequence for 1179 amplification primer Selected sequences  ACGGCATCT AGTAAGCTGC T 1181 for amplification                               CCAAAG GATCTCTTGC AGTT 1182 primers^(a) Selected sequence for 1180 hybridization probe^(a) The sequence numbering refers to the Streptococcus pneumoniae hexA gene fragment (SEQ ID NO. 1183). Nucleotides in capitals are identical to the selected sequences or match those sequences. Mismatches are indicated by lower-case letters. Dots indicate gaps in the sequences displayed. “—” indicate incomplete sequence data. ^(a)This sequence is the reverse-complement of the selected primer.

Annex XLIII: Specific and ubiquitous primers for nucleic acid amplification (pcp sequence). Originating DNA fragment SEQ SEQ ID Nucleotide ID NO. Nucleotide sequence NO. position Bacterial species: Streptococcus pyogenes 1211 5′-ATT CTT GTA ACA GGC TTT 1215^(a) 291-314 GAT CCC 1210^(b) 5′-ACC AGC TTG CCC AAT ACA 1215^(a) 473-494 AAG G ^(a)Sequences from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Annex XLIV: Specific and ubiquitous primers for nucleic acid amplification of S. saprophyticus sequences of unknown coding potential. Originating DNA fragment SEQ ID SEQ ID Nucleotide NO. Nucleotide sequence NO. position Bacterial species: Staphylococcus saprophyticus 1208 5′-TCA AAA AGT TTT CTA 74, 1093, 169-193^(c) AAA AAT TTA C 1198^(b) 1209^(a) 5′-ACG GGC GTC CAC AAA 74, 1093, 355-379^(c) ATC AAT AGG A 1198^(b) ^(a)This sequence is from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(b)These sequences were aligned to derive the corresponding primer. ^(c)The nucleotide positions refer to the S. saprophyticus unknown gene sequence fragment (SEQ ID NO. 1198).

Annex XLV: Molecular beacon internal hybridization probes for specific detection of antimicrobial agents resistance gene sequences. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence^(a) NO. position Resistance gene: gyrA 2250 5′-CCG TCG GAT GGT GTC GTA TAC CGC GGA GTC 1954^(b) 218-243 GCC GAC GG 2251 5′-CGG AGC CGT TCT CGC TGC GTT ACA TGC TGG 1954^(b) 259-286 TGG CTC CG Resistance gene: mecA 1231 5′-GCG AGC CCG AAG ATA AAA AAG AAC CTC TGC 1178^(b) 1291-1315 TGC TCG C Resistance gene: parC 1938^(b) 5′-CCG CGC ACC ATT GCT TCG TAC ACT GAG GAG 1321^(c) 232-260 TCT CCG CGC GG 1939 5′-CGA CCC GGA TGG TAG TAT CGA TAA TGA TCC 1321^(c) 317-346 GCC AGC GGC CGG GTC G 1955^(b) 5′-CGC GCA ACC ATT GCT TCG TAC ACT GAG GAG 1321^(c) 235-260 TCT GCG CG Resistance gene: vanA 1239 5′-GCG AGC GCA GAC CTT TCA GCA GAG GAG GCT 1051 860-880 CGC 1240 5′-GCG AGC CGG CAA GAC AAT ATG ACA GCA AAA 1051 663-688 TCG CTC GC Resistance gene: vanB 1241 5′-GCG AGC GGG GAA CGA GGA TGA TTT GAT TGG 1117 555-577 CTC GC Resistance gene: vanD 1593 5′-CCG AGC GATTTA CCG GAT ACT TGG CTG ICG 1594 835-845 CTC GG ^(a)Underlined nucleotides indicate the molecular beacon's stem. ^(b)This sequence is from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(c)Sequence from databases.

Annex XLVI: Molecular beacon internal hybridization probe for specific detection of S. aureus gene sequences of unknown coding potential. Originating DNA fragment SEQ SEQ ID ID Nucleotide NO. Nucleotide sequence^(a) NO. position Bacterial species: S. aureus 1232 5′-GGA GCC GCG CGA TTT TAT 1244 53-80 AAA TGA ATG TTG ATA ACC GGC TCC ^(a)Underlined nucleotides indicate the molecular beacon's stem.

Annex XLVII: Molecular beacon internal hybridization probes for specific detection of tuf sequences. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence^(a) NO. position Bacterial species: Chlamydia pneumoniae 2091 5′-CGC GAC TTG AGA TGG AAC TTA GTG AGC  20 157-183 TTC TTG GTC GCG 2092 5′-CGC GAC GAA AGA ACT TCC TGA AGG TCG  20 491-516 TGC AGG TCC AG Bacterial species: Chlamydia trachomatis 2213 5′-CGT GCC ATT GAC ATG ATT TCC GAA GAA 1739^(b) 412-441 GAC GCT GAA GGC ACG Bacterial species: Enterococcus faecalis 1236 5′-GCG AGC CGT GGT GAA GTT CGC GTT GGT 883 370-391 GGC TCG C Bacterial species: Enterococcus faecium 1235 5′-GCG AGC CGA AGT TGA AGT TGT TGG TAT  64 412-437 TGC TGG CTC GC Bacterial species: Legionella pneumophila 2084^(c) 5′-CAC GCG TCA ACA CCC GTA CAA GTC GTC 112 461-486 TTT TGC GCG TG Bacterial species: Mycoplasma pneumoniae 2096^(c) 5′-CGC GAC CGG TAC CAC GGC CAG TAA TCG 2097^(b) 658-679 TGT CGC G Bacterial species: Neisseria gonorrhoeae 2177 5′-GGC ACG GAC AAA CCA TTC CTG CTG CCT 126 323-357 ATC GAA ACG TGT TCC CGT GCC 2178 5′-GGC ACG ACA AAC CAT TCC TGC TGC CTA 126 323-348 TCG AAC GTG CC 2179 5′-GGC AGC TCT ACT TCC GTA CCA CTG ACG 126 692-718 TAA CCG GCT GCC ^(a)Underlined nucleotides indicate the molecular beacon's stem. ^(b)Sequence from databases. ^(c)This sequence is from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence^(a) NO. position Bacterial species: Pseudomonas aeruginosa 2122 5′-CCG AGC GAA TGT AGG AGT CCA GGG TCT 153, 280-302^(d) CTG CTC GG 880, 2138^(b,c) Bacterial species: Staphylococcus aureus 2186 5′-ACG CGC TCA AAG CAG AAG TAT ACG TAT 1728  615-646 TAT CAA AAG ACG CGC GT Bacterial group: Staphylococcus sp. other than S. aureus 1233 5′-GCG AGC GTT ACT GGT GTA GAA ATG TTC 878 372-394 CGG CTC GC Fungal species: Candida albicans 2073 5′-CCG AGC AAC ATG ATT GAA CCA TCC ACC 408 404-429 AAC TGG CTC GG Fungal species: Candida dubliniensis 2074 5′-CCG AGC AAC ATG ATT GAA GCT TCC ACC 414 416-441 AAC TGG CTC GG Fungal species: Candida glabrata 2110^(b) 5′-GCG GGC CCT TAA CGA TTT CAG CGA ATC 417 307-335 TGG ATT CAG CCC GC 2111 5′-GCG GGC ATG TTG AAG CCA CCA CCA ACG 417 419-447 CTT CCT GGC CCG C Fungal species: Candida krusei 2112^(b) 5′-GCG GGC TTG ATG AAG TTT GGG TTT CCT 422 318-347 TGA CAA TTG CCC GC 2113 5′-GCG GGC ACA AGG GTT GGA CTA AGG AAA 422 419-447 CCA AGG CAG CCC GC 2114 5′-GCG GGC ATC GAT GCT ATT GAA CCA CCT 422 505-533 GTC AGA CCG CCC GC ^(a)Underlined nucleotides indicate the molecular beacon's stem. ^(b)Sequence from databases. ^(c)These sequences were aligned to derive the corresponding primer. ^(d)The nucleotide positions refer to the P. aeruginosa tuf sequence fragment (SEQ ID NO. 153). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence^(a) NO. position Fungal species: Candida lusitaniae 2115^(b) 5′-GCG GGC GGT AAG TCC ACC GGT AAG ACC 424 304-330 TTG TTG GCC CGC 2116 5′-GCG GGC GTA AGT CAC CGG TAA GAC CTT 424 476-502 GTT GGC CCG C 2117 5′-GCG GGC GAC GCC ATT GAG CCA CCT TCG 424 512-535 AGA GCC CGC Fungal species: Candida parapsilosis 2118^(b) 5′-GCG GGC TCC TTG ACA ATT TCT TCG TAT 426 301-330 CTG TTC TTG GCC CGC Fungal species: Candida tropicalis 2119 5′-GCG GGC TTA CAA CCC TAA GGC TGT TCC 429 357-384 ATT CGT TGC CCG C 2120 5′-GCG GGC AGA AAC CAA GGC TGG TAA GGT 429 459-487 TAC CGG AGC CCG C Fungal species: Cryptococcus neoformans 2106 5′-GCG AGC AGA GCA CGC CCT CCT CGC CGC 623,  226-244^(d) TCG C 1985, 1986^(c) 2107 5′-GCG AGC TCC CCA TCT CTG GTT GGC ACG 623,  390-408^(d) CTC GC 1985, 1986^(c) Bacterial genus: Legionella sp. 2083 5′-CCG CCG ATG TTC CGT AAA TTA CTT GAI 111-112^(d)  488-519^(e) GAA GGT CGA GCC GGC GG ^(a)Underlined nucleotides indicate the molecular beacon's stem. ^(b)This sequence is from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing. ^(c)These sequences were aligned to derive the corresponding primer. ^(d)The nucleotide positions refer to the C. neoformans tuf (EF-1) sequence fragment (SEQ ID NO. 623). ^(e)The nucleotide positions refer to the L. pneumophila tuf (EF-1) sequence fragment (SEQ ID NO. 112). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence^(a) NO. position Fungal genus: Candida sp. 2108 5′-GCG GGC AAC TTC RTC AAG AAG GTT GGT 414,  52-80^(c) TAC AAC CCG CCC GC 417, 422, 424, 426, 429, 624^(b) 2109 5′-GCGP GGC CCA ATC TCT GGT TGG AAY GGT Same as  100-125^(c) GAC AAG CCC GC SEQ ID NO. 2108 Bacterial group: Pseudomonads 2121 5′-CGA CCG CIA GCC GCA CAC CAA GTT CCG 153-  598-616^(e) GTC G 155, 205, 880, 2137^(d,) 2138^(d,b) ^(a)Underlined nucleotides indicate the molecular beacon's stem. ^(b)These sequences were aligned to derive the corresponding primer. ^(c)The nucleotide positions refer to the C. albicans tuf (EF-1) sequence fragment (SEQ ID NO. 624). ^(d)Sequence from databases. ^(e)The nucleotide positions refer to the P. aeruginosa tuf sequence fragment (SEQ ID NO. 153).

Annex XLVIII: Molecular beacon internal hybridization probes for specific detection of ddl and mtl gene sequences. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence^(a) NO. position Bacterial species: E. faecium (ddl) 1237 5′-GCG AGC CGC GAA ATC GAA GTT GCT GTA 1242^(b) 334-359 TTA GGG CTC GC Bacterial species: E. faecalis (mtl) 1238 5′-GCG AGC GGC GTT AAT TTT GGC ACC GAA 1243^(b) 631-656 GAA GAG CTC GC ^(a)Underlined nucleotides indicate the molecular beacon's stem. ^(b)Sequence from databases.

Annex XLIX: Internal hybridization probe for specific detection of S. aureus sequences of unknown coding potential. Originating DNA fragment SEQ SEQ ID ID Nucleotide NO. Nucleotide sequence NO. position Bacterial species: Staphylococcus aureus 1234 5′-ACT AAA TAA ACG CTC ATT CG 1244 35-54

Annex L: Specific and ubiquitous primers for nucleic acid amplification (antimicrobial agents resistance genes sequences). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Resistance gene: aac(2′)-Ia 1344 5′-AGC AGC AAC GAT GTT ACG CAG CAG 1348^(a) 163-186 1345^(b) 5′-CCC GCC GAG CAT TTC AAC TAT TG 1348^(a) 392-414 1346 5′-GAT GTT ACG CAG CAG GGC AGT C 1348^(a) 172-193 1347^(b) 5′-ACC AAG CAG GTT CGC AGT CAA GTA 1348^(a) 467-490 Resistance gene: aac(3′)-Ib 1349 5′-CAG CCG ACC AAT GAG TAT CTT GCC 1351^(a) 178-201 1350^(b) 5′-TAA TCA GGG CAG TTG CGA CTC CTA 1351^(a) 356-379 Resistance gene: aac(3′)-IIb 1352 5′-CCA CGC TGA CAG AGC CGC ACC G 1356^(a) 383-404 1353^(b) 5′-GGC CAG CTC CCA TCG GAC CCT G 1356^(a) 585-606 1354 5′-CAC GCT GAC AGA GCC GCA CCG 1356^(a) 384-404 1355^(b) 5′-ATG CCG TTG CTG TCG AAA TCC TCG 1356^(a) 606-629 Resistance gene: aac(3′)-IVa 1357 5′-GCC CAT CCA TTT GCC TTT GC 1361^(a) 295-314 1358^(b) 5′-GCG TAC CAA CTT GCC ATC CTG AAG 1361^(a) 517-540 1359 5′-TGC CCC TGC CAC CTC ACT C 1361^(a) 356-374 1360^(b) 5′-CGT ACC AAC TTG CCA TCC TGA AGA 1361^(a) 516-539 Resistance gene: aac(3′)-VIa 1362 5′-CGC CGC CAT CGC CCA AAG CTG G 1366^(a) 285-306 1363^(b) 5′-CGG CAT AAT GGA GCG CGG TGA CTG 1366^(a) 551-574 1364 5′-TTT CTC GCC CAC GCA GGA AAA ATC 1366^(a) 502-525 1365^(b) 5′-CAT CCT CGA CGA ATA TGC CGC G 1366^(a) 681-702 Resistance gene: aac(6′)-Ia 1367 5′-CAA ATA TAC TAA CAG AAG CGT TCA 1371^(a) 56-79 1368^(b) 5′-AGG ATC TTG CCA ATA CCT TTA T 1371^(a) 269-290 1379 5′-AAA CCT TTG TTT CGG TCT GCT AAT 1371^(a) 153-176 1380^(b) 5′-AAG CGA TTC CAA TAA TAC CTT GCT 1371^(a) 320-343 Resistance gene: aac(6′)-Ic 1372 5′-GCT TTC GTT GCC TTT GCC GAG GTC 1376^(a) 157-180 1373^(b) 5′-CAC CCC TGT TGC TTC GCC CAC TC 1376^(a) 304-326 1374 5′-AGA TAT TGG CTT CGC CGC ACC ACA 1376^(a) 104-127 1375^(b) 5′-CCC TGT TGC TTC GCC CAC TCC TG 1376^(a) 301-323 Resistance gene: ant(3′)-Ia 1377 5′-GCC GTG GGT CGA TGT TTG ATG TTA 1381^(a) 100-123 1378^(b) 5′-GCT CGA TGA CGC CAA CTA CCT CTG 1381^(a) 221-244 1379 5′-AGC AGC AAC GAT GTT ACG CAG CAG 1381^(a) 127-150 1380^(b) 5′-CGC TCG ATG ACG CCA ACT ACC TCT 1381^(a) 222-245 Resistance gene: ant(4′)-Ia 1382 5′-TAG ATA TGA TAG GCG GTA AAA AGC 1386^(a) 149-172 1383^(b) 5′-CCC AAA TTC GAG TAA GAG GTA TT 1386^(a) 386-408 1384 5′-GAT ATG ATA GGC GGT AAA AAG C 1386^(a) 151-172 1385^(b) 5′-TCC CAA ATT CGA GTA AGA GGT A 1386^(a) 388-409 Resistance gene: aph(3′)-Ia 1387 5′-TTA TGC CTC TTC CGA CCA TCA AGC 1391^(a) 233-256 1338^(b) 5′-TAC GCT CGT CAT CAA AAT CAC TCG 1391^(a) 488-511 1389 5′-GAA TAA CGG TTT GGT TGA TGC GAG 1391^(a) 468-491 1390^(b) 5′-ATG GCA AGA TCC TGG TAT CGG TCT 1391^(a) 669-692 Resistance gene: aph(3′)-IIa 1392 5′-TGG GTG GAG AGG CTA TTC GGC TAT 1396^(a) 43-66 1393^(b) 5′-CAG TCC CTT CCC GCT TCA GTG AC 1396^(a) 250-272 1394 5′-GAC GTT GTC ACT GAA GCG GGA AGG 1396^(a) 244-267 1395^(b) 5′-CTT GGT GGT CGA ATG GGC AGG TAG 1396^(a) 386-409 Resistance gene: aph(3′)-IIIa 1397 5′-GTG GGA GAA AAT GAA AAC CTA T 1401^(a) 103-124 1398^(b) 5′-ATG GAG TGA AAG AGC CTG AT 1401^(a) 355-374 1399 5′-ACC TAT GAT GTG GAA CGG GAA AAG 1401^(a) 160-183 1400^(b) 5′-CGA TGG AGT GAA AGA GCC TGA TG 1401^(a) 354-376 Resistance gene: aph(3′)-VIa 1402 5′-TAT TCA ACA ATT TAT CGG AAA CAG 1406^(a) 18-41 1403^(b) 5′-TCA GAG AGC CAA CTC AAC ATT TT 1406^(a) 175-197 1404 5′-AAA CAG CGT TTT AGA GCC AAA TAA 1406^(a) 36-59 1405^(b) 5′-TTC TCA GAG AGC CAA CTC AAC ATT 1406^(a) 177-200 Resistance gene: blaCARB 1407 5′-CCC TGT AAT AGA AAA GCA AGT AGG 1411^(a) 351-374 1408^(b) 5′-TTG TCG TAT CCC TCA AAT CAC C 1411^(a) 556-577 1409 5′-TGG GAT TAC AAT GGC AAT CAG CG 1411^(a) 205-227 1410^(b) 5′-GGG GAA TAG GTC ACA AGA TCT GCT T 1411^(a) 329-353 Resistance gene: blaCMY-2 1412 5′-GAG AAA ACG CTC CAG CAG GGC 1416^(a) 793-813 1413^(b) 5′-CAT GAG GCT TTC ACT GCG GGG 1416^(a) 975-995 1414 5′-TAT CGT TAA TCG CAC CAT CAC 1416^(a)  90-110 1415^(b) 5′-ATG CAG TAA TGC GGC TTT ATC 1416^(a) 439-459 Resistance genes: blaCTX-M-1, blaCTX-M-2 1417 5′-TGG TTA ACT AYA ATC CSA TTG CGG A 1423^(a) 314-338 1418^(b) 5′-ATG CTT TAC CCA GCG TCA GAT T 1423^(a) 583-604 Resistance gene: blaCTX-M-1 1419 5′-CGA TGA ATA AGC TGA TTT CTC ACG 1423^(a) 410-433 1420^(b) 5′-TGC TTT ACC CAG CGT CAG ATT ACG 1423^(a) 580-603 1421 5′-AAT TAG AGC GGC AGT CGG GAG GAA 1423^(a) 116-139 1422^(b) 5′-GAA ATC AGC TTA TTC ATC GCC ACG 1423^(a) 405-428 Resistance gene: b1aCTX-M-2 1424 5′-GTT AAC GGT GAT GGC GAC GCT AC 1428^(a) 30-52 1425^(b) 5′-GAA TTA TCG GCG GTG TTA ATC AGC 1428^(a) 153-176 1426 5′-CAC GCT CAA TAC CGC CAT TCC A 1428^(a) 510-531 1427^(b) 5′-TTA TCG CCC ACT ACC CAT GAT TTC 1428^(a) 687-710 Resistance gene: b1aIMP 1429 5′-TTT ACG GCT AAA GAT ACT GAA AAG T 1433^(a) 205-229 1430^(b) 5′-GTT TAA TAA AAC AAC CAC CGA ATA AT 1433^(a) 513-538 1431 5′-TAA TTG ACA CTC CAT TTA CGG CTA A 1433^(a) 191-215 1432^(b) 5′-ACC GAA TAA TAT TTT CCT TTC AGG CA 1433^(a) 497-522 Resistance gene: b1aOXA2 1434 5′-CAC AAT CAA GAC CAA GAT TTG CGA T 1438^(a) 319-343 1435^(b) 5′-GAA AGG GCA GCT CGT TAC GAT AGA G 1438^(a) 532-556 Resistance gene: b1aOXA10 1436 5′-CAG CAT CAA CAT TTA AGA TCC CCA 1439^(a) 194-217 1437^(b) 5′-CTC CAC TTG ATT AAC TGC GGA AAT TC 1439^(a) 479-504 Resistance gene: b1aPER-1 1440 5′-AGA CCG TTA TCG TAA ACA GGG CTA AG 1442^(a) 281-306 1441^(b) 5′-TTT TTT GCT CAA ACT TTT TCA GGA TC 1442^(a) 579-604 Resistance gene: b1aPER-2 1443 5′-CTT CTG CTC TGC TGA TGC TTG GC 1445^(a) 32-54 1444^(b) 5′-GGC GAC CAG GTA TTT TGT AAT ACT GC 1445^(a) 304-329 Resistance genes: b1aPER-1, b1aPER-2 1446 5′-GGC CTG YGA TTT GTT ATT TGA ACT GGT 1442^(a) 414-440 1447^(b) 5′-CGC TST GGT CCT GTG GTG GTT TC 1442^(a) 652-674 1448 5′-GAT CAG GTG CAR TAT CAA AAC TGG AC 1442^(a) 532-557 1449^(b) 5′-AGC WGG TAA CAA YCC TTT TAA CCG CT 1442^(a) 671-696 Resistance gene: b1aSHV 1883 5′-AGC CGC TTG AGC AAA TTA AAC TA 1900^(a) 71-93 1884^(b) 5′-GTA TCC CGC AGA TAA ATC ACC AC 1900^(a) 763-785 1885 5′-AGC GAA AAA CAC CTT GCC GAC 1900^(a) 313-333 1884^(b) 5′-GTA TCC CGC AGA TAA ATC ACC AC 1900^(a) 763-785 Resistance gene: b1aTEM 1906 5′-CCT TAT TCC CTT TTT TGC GG 1927^(a) 27-46 1907^(b) 5′-CAC CTA TCT CAG CGA TCT GTC T 1927^(a) 817-838 1908 5′-AAC AGC GGT AAG ATC CTT GAG AG 1927^(a) 148-170 1907^(b) 5′-CAC CTA TCT CAG CGA TCT GTC T 1927^(a) 817-838 Resistance gene: catI 2145 5′-GCA AGA TGT GGC GTG TTA CGG T 2147^(a) 363-384 2146^(b) 5′-GGG GCG AAG AAG TTG TCC ATA TT 2147^(a) 484-506 Resistance gene: catII 2148 5′-CAG ATT AAA TGC GGA TTC AGC C 2150^(a) 67-88 2149^(b) 5′-ATC AGG TAA ATC ATC AGC GGA TA 2150^(a) 151-173 Resistance gene: catIII 2151 5′-ATA TTT CAG CAT TAC CTT GGG TT 2153^(a) 419-441 2152^(b) 5′-TAC ACA ACT CTT GTA GCC GAT TA 2153^(a) 603-625 Resistance gene: catP 2154 5′-CGC CAT TCA GAG TTT AGG AC 2156^(a) 178-197 2155^(b) 5′-TTC CAT ACC GTT GCG TAT CAC TT 2156^(a) 339-361 Resistance gene: cat 2157 5′-CCA CAG AAA TTG ATA TTA GTG TTT TAT 2159^(a)  89-115 2158^(b) 5′-TCG CTA TTG TAA CCA GTT CTA 2159^(a) 201-221 2160 5′-TTT TGA ACA CTA TTT TAA CCA GC 2162^(a) 48-70 2161^(b) 5′-GAT TTA ACT TAT CCC AAT AAC CT 2162^(a) 231-253 Resistance gene: dfrA 1450 5′-ACC ACT GGG AAT ACA CTT GTA ATG GC 1452^(a) 106-131 1451^(b) 5′-ATC TAC CTG GTC AAT CAT TGC TTC GT 1452^(a) 296-321 Resistance gene: dhfrIa 1457 5′-CAA AGG TGA ACA GCT CCT GTT T 1461^(a) 75-96 1458^(b) 5′-TCC GTT ATT TTC TTT AGG TTG GTT AAA 1461^(a) 249-275 1459 5′-AAG GTG AAC AGC TCC TGT TT 1461^(a) 77-96 1560^(b) 5′-GAT CAC TAC GTT CTC ATT GTC A 1461^(a) 207-228 Resistance genes: dhfrIa, dhfrXV 1453 5′-ATC GAA GAA TGG AGT TAT CGG RAA TG 1461^(a) 27-52 1454^(b) 5′-CCT AAA AYT RCT GGG GAT TTC WGG A 1461^(a) 384-408 1455 5′-CAG GTG GTG GGG AGA TAT ACA AAA 1461^(a) 290-313 1456^(b) 5′-TAT GTT AGA SRC GAA GTC TTG GKT AA 1461^(a) 416-441 Resistance gene: dhfrIb 1466 5′-AAG CAT TGA CCT ACA ATC AGT GT 1470^(a)  98-120 1467^(b) 5′-AAT ACA ACT ACA TTG TCA TCA TTT GAT 1470^(a) 204-230 1468 5′-CGT TAC CCG CTC AGG TTG GAC ATC AA 1470^(a) 183-208 1469^(b) 5′-CAT CCC CCT CTG GCT CGA TGT CG 1470^(a) 354-376 Resistance gene: dhfrV 1471 5′-GAT AAT GAC AAC GTA ATA GTA TTC CC 1475^(a) 208-233 1472^(b) 5′-GCT CAA TAT CAA TCG TCG ATA TA 1475^(a) 342-364 1473 5′-TTA AAG CCT TGA CGT ACA ACC AGT GG 1475^(a)  95-120 1474^(b) 5′-TGG GCA ATG TTT CTC TGT AAA TCT CC 1475^(a) 300-325 Resistance genes: dhfrIb, dhfrV 1462 5′-GCA CTC CCY AAT AGG AAA TAC GC 1470^(a) 157-179 1463^(b) 5′-AGT GTT GCT CAA AAA CAA CTT CG 1470^(a) 405-427 1464 5′-ACG TTY GAA TCT ATG GGM GCA CT 1470^(a) 139-161 1465^(b) 5′-GTC GAT AAG TGG AGC GTA GAG GC 1470^(a) 328-350 Resistance gene: dhfrVI 1476 5′-GGC GAG CAG CTC CTA TTC AAA G 1480^(a)  79-100 1477^(b) 5′-TAG GTA AGC TAA TGC CGA TTC AAC A 1480^(a) 237-261 1478 5′-GAG AAT GGA GTA ATT GGC TCT GGA TT 1480^(a) 31-56 1479^(b) 5′-GCG AAA TAC ACA ACA TCA GGG TCA T 1480^(a) 209-233 Resistance gene: dhfrVII 1485 5′-AAA ATG GCG TAA TCG GTA ATG GC 1489^(a) 32-54 1486^(b) 5′-CAT TTG AGC TTG AAA TTC CTT TCC TC 1489^(a) 189-214 1487 5′-AAT CGA AAA TAT GCA GTA GTG TCG AG 1489^(a) 166-191 1488^(b) 5′-AGA CTA TTG TAG ATT TGA CCG CCA 1489^(a) 294-317 Resistance genes: dhfrVII, dhfrXVII 1481 5′-RTT ACA GAT CAT KTA TAT GTC TCT 1489^(a) 268-291 1482^(b) 5′-TAA TTT ATA TTA GAC AWA AAA AAC TG 1489^(a) 421-446 1483 5′-CAR YGT CAG AAA ATG GCG TAA TC 1489^(a) 23-45 1484^(b) 5′-TKC AAA GCR WTT TCT ATT GAA GGA AA 1489^(a) 229-254 Resistance gene: dhfrVIII 1490 5′-GAC CTA TGA GAG CTT GCC CGT CAA A 1494^(a) 144-168 1491^(b) 5′-TCG CCT TCG TAC AGT CGC TTA ACA AA 1494^(a) 376-401 1492 5′-CAT TTT AGC TGC CAC CGC CAA TGG TT 1494^(a) 18-43 1493^(b) 5′-GCG TCG CTG ACG TTG TTC ACG AAG A 1494^(a) 245-269 Resistance gene: dhfrIX 1495 5′-TCT CTA AAC ATG ATT GTC GCT GTC 1499^(a)  7-30 1496^(b) 5′-CAG TGA GGC AAA AGT TTT TCT ACC 1499^(a) 133-156 1497 5′-CGG ACG ACT TCA TGT GGT AGT CAG T 1499^(a) 171-195 1498^(b) 5′-TTT GTT TTC AGT AAT GGT CGG GAC CT 1499^(a) 446-471 Resistance gene: dhfrXII 1500 5′-ATC GGG TTA TTG GCA ATG GTC CTA 1504^(a) 50-73 1501^(b) 5′-GCG GTA GTT AGC TTG GCG TGA GAT T 1504^(a) 201-225 1502 5′-GCG GGC GGA GCT GAG ATA TAC A 1504^(a) 304-325 1503^(b) 5′-AAC GGA GTG GGT GTA CGG AAT TAC AG 1504^(a) 452-477 Resistance gene: dhfrXIII 1505 5′-ATT TTT CGC AGG CTC ACC GAG AGC 1507^(a) 106-129 1506^(b) 5′-CGG ATG AGA CAA CCT CGA ATT CTG CTG 1507^(a) 413-439 Resistance gene: dhfrXV 1508 5′-AGA ATG TAT TGG TAT TTC CAT CTA TCG 1512^(a) 215-241 1509^(b) 5′-CAA TGT CGA TTG TTG AAA TAT GTA AA 1512^(a) 336-361 1510 5′-TGG AGT GCC AAA GGG GAA CAA T 1512^(a) 67-88 1511^(b) 5′-CAG ACA CAA TCA CAT GAT CCG TTA TCG 1512^(a) 266-292 Resistance gene: dhfrXVII 1513 5′-TTC AAG CTC AAA TGA AAA CGT CC 1517^(a) 201-223 1514^(b) 5′-GAA ATT CTC AGG CAT TAT AGG GAA T 1517^(a) 381-405 1515 5′-GTG GTC AGT AAA AGG TGA GCA AC 1517^(a) 66-88 1516^(b) 5′-TCT TTC AAA GCA TTT TCT ATT GAA GG 1517^(a) 232-257 Resistance gene: embB 2102 5′-CAC CTT CAC CCT GAC CGA CG 2105^(a) 822-841 2103^(b) 5′-CGA ACC AGC GGA AAT AGT TGG AC 2105^(a) 948-970 Resistance genes: ereA, ereA2 1528 5′-AAC TTG AGC GAT TTT CGG ATA CCC TG 1530^(a)  80-105 1529^(b) 5′-TTG CCG ATG AAA TAA CCG CCG ACT 1530^(a) 317-340 Resistance gene: ereB 1531 5′-TCT TTT TGT TAC GAC ATA CGC TTT T 1535^(a) 152-176 1532^(b) 5′-AGT GCT TCT TTA TCC GCT GTT CTA 1535^(a) 456-479 1533 5′-CAG CGG ATA AAG AAG CAC TAC ACA TT 1535^(a) 461-486 1534^(b) 5′-CCT CCT GAA ATA AAG CCC GAC AT 1535^(a) 727-749 Resistance gene: gyrA 1340 5′-GAA CAA GGT ATG ACA CCG GAT AAA T 1299^(a) 163-188 1341^(b) 5′-GAT AAC TGA AAT CCT GAG CCA TAC G 1299^(a) 274-299 1936 5′-TAC CAC CCG CAC GGC 1954^(a) 205-219 1937^(b) 5′-CGG AGT CGC CGT CGA TG 1954^(a) 309-325 1942 5′-GAC TGG AAC AAA GCC TAT AAA AAA TCA 1954^(a) 148-174 1937^(b) 5′-CGG AGT CGC CGT CGA TG 1954^(a) 309-325 2040 5′-TGT GAC CCC AGA CAA ACC C 2054^(a) 33-51 2041^(b) 5′-GTT GAG CGG CAG CAC TAT CT 2054^(a) 207-226 Resistance gene: inhA 2098 5′-CTG AGT CAC ACC GAC AAA CGT C 2101^(a) 910-931 2099^(b) 5′-CCA GGA CTG AAC GGG ATA CGA A 2101^(a) 1074-1095 Resistance genes: linA, linA′ 1536 5′-AGA TGT ATT AAC TGG AAA ACA ACA A 1540^(a)  99-123 1537^(b) 5′-CTT TGT AAT TAG TTT CTG AAA ACC A 1540^(a) 352-376 1538 5′-TTA GAA GAT ATA GGA TAC AAA ATA GAA G 1540^(a) 187-214 1539^(b) 5′-GAA TGA AAA AGA AGT TGA GCT T 1540^(a) 404-425 Resistance gene: linB 1541 5′-TGA TAA TCT TAT ACG TGG GGA ATT T 1545^(a) 246-270 1542^(b) 5′-ATA ATT TTC TAA TTG CCC TGT TTC AT 1545^(a) 359-384 1543 5′-GGG CAA TTA GAA AAT TAT TTA TCA GA 1545^(a) 367-392 1544^(b) 5′-TTT TAC TCA TGT TTA GCC AAT TAT CA 1545^(a) 579-604 Resistance gene: mefA 1546 5′-CAA GAA GGA ATG GCT GTA CTA C 1548^(a) 625-646 1547^(b) 5′-TAA TTC CCA AAT AAC CCT AAT AAT AGA 1548^(a) 816-842 Resistance gene: mefE 1549 5′-GCT TAT TAT TAG GAA GAT TAG GGG GC 1551^(a) 815-840 1550^(b) 5′-TAG CAA GTG ACA TGA TAC TTC CGA 1551^(a) 1052-1075 Resistance genes: mefA, mefE 1552 5′-GGC AAG CAG TAT CAT TAA TCA CTA 1548^(a) 50-73 1553^(b) 5′-CAA TGC TAC GGA TAA ACA ATA CTA TC 1548^(a) 318-343 1554 5′-AGA AAA TTA AGC CTG AAT ATT TAG GAC 1548^(a) 1010-1035 1555^(b) 5′-TAG TAA AAA CCA ATG ATT TAC ACC G 1548^(a) 1119-1143 Resistance genes: mphA, mphK 1556 5′-ACT GTA CGC ACT TGC AGC CCG ACA T 1560^(a) 33-57 1557^(b) 5′-GAA CGG CAG GCG ATT CTT GAG CAT 1560^(a) 214-237 1558 5′-GTG GTG GTG CAT GGC GAT CTC T 1560^(a) 583-604 1559^(b) 5′-GCC GCA GCG AGG TAC TCT TCG TTA 1560^(a) 855-878 Resistance gene: mupA 2142 5′-GCC TTA ATT TCG GAT AGT GC 2144^(a) 1831-1850 2143^(b) 5′-GAG AAA GAG CCC AAT TAT CTA ATG T 2144^(a) 2002-2026 Resistance gene: parC 1342 5′-GAT GTT ATT GGT CAA TAT CAT CCA 1321^(a) 205-229 1343^(b) 5′-AAG AAA CTG TCT CTT TAT TAA TAT CAC GT 1321^(a) 396-425 1934 5′-GAA CGC CAG CGC GAA ATT CAA AAA G 1781 67-91 1935^(b) 5′-AGC TCG GCA TAC TTC GAC AGG 1781 277-297 2044 5′-ACC GTA AGT CGG CCA AGT CA 2055^(a) 176-195 2045^(b) 5′-GTT CTT TCT CCG TAT CGT C 2055^(a) 436-454 Resistance gene: ppflo-like 2163 5′-ACC TTC ATC CTA CCG ATG TGG GTT 2165^(a) 922-945 2164^(b) 5′-CAA CGA CAC CAG CAC TGC CAT TG 2165^(a) 1136-1158 Resistance gene: rpoB 2065 5′-CCA GGA CGT GGA GGC GAT CAC A 2072^(a) 1218-1239 2066^(b) 5′-CAC CGA CAG CGA GCC GAT CAG A 2072^(a) 1485-1506 Resistance gene: satG 1581 5′-AAT TGG GGA CTA CAC CTA TTA TGA TG 1585^(a)  93-118 1582^(b) 5′-GGC AAA TCA GTC AGT TCA GGA GT 1585^(a) 310-332 1583 5′-CGA TTG GCA ACA ATA CAC TCC TG 1585^(a) 294-316 1584^(b) 5′-TCA CCT ATT TTT ACG CCT GGT AGG AC 1585^(a) 388-413 Resistance gene: sulII 1961 5′-GCT CAA GGC AGA TGG CAT TCC C 1965^(a) 222-243 1962^(b) 5′-GGA CAA GGC GGT TGC GTT TGA T 1965^(a) 496-517 1963 5′-CAT TCC CGT CTC GCT CGA CAG T 1965^(a) 237-258 1964^(b) 5′-ATC TGC CTG CCC GTC TTG C 1965^(a) 393-411 Resistance gene: tetB 1966 5′-CAT GCC AGT CTT GCC AAC G 1970^(a) 66-84 1967^(b) 5′-CAG CAA TAA GTA ATC CAG CGA TG 1970^(a) 242-264 1968 5′-GGA GAG ATT TCA CCG CAT AG 1970^(a) 457-476 1969^(b) 5′-AGC CAA CCA TCA TGC TAT TCC A 1970^(a) 721-742 Resistance gene: tetM 1586 5′-ATT CCC ACA ATC TTT TTT ATC AAT AA 1590^(a) 361-386 1587^(b) 5′-CAT TGT TCA GAT TCG GTA AAG TTC 1590^(a) 501-524 1588 5′-GTT TTT GAA GTT AAA TAG TGT TCT T 1590^(a) 957-981 1589^(b) 5′-CTT CCA TTT GTA CTT TCC CTA 1590^(a) 1172-1192 Resistance gene: vatB 1609 5′-GCC CTG ATC CAA ATA GCA TAT A 1613^(a) 11-32 1610^(b) 5′-CCT GGC ATA ACA GTA ACA TTC TG 1613^(a) 379-401 1611 5′-TGG GAA AAA GCA ACT CCA TCT C 1613^(a) 301-322 1612^(b) 5′-ACA ACT GAA TTC GCA GCA ACA AT 1613^(a) 424-446 Resistance gene: vatC 1614 5′-CCA ATC CAG AAG AAA TAT ACC C 1618^(a) 26-47 1615^(b) 5′-ATT AGT TTA TCC CCA ATC AAT TCA 1618^(a) 177-200 1616 5′-ATA ATG AAT GGG GCT AAT CAT CGT AT 1618^(a) 241-266 1617^(b) 5′-GCC AAC AAC TGA ATA AGG ATC AAC 1618^(a) 463-486 Resistance gene: vga 1619 5′-AAG GCA AAA TAA AAG GAG CAA AGC 1623^(a) 641-664 1620^(b) 5′-TGT ACC CGA GAC ATC TTC ACC AC 1623^(a) 821-843 1621 5′-AAT TGA AGG ACG GGT ATT GTG GAA AG 1623^(a) 843-868 1622^(b) 5′-CGA TTT TGA CAG ATG GCG ATA ATG AA 1623^(a) 975-1000 Resistance gene: vgaB 1624 5′-TTC TTT AAT GCT CGT AGA TGA ACC TA 1628^(a) 354-379 1625^(b) 5′-TTT TCG TAT TCT TCT TGT TGC TTT C 1628^(a) 578-602 1626 5′-AGG AAT GAT TAA GCC CCC TTC AAA AA 1628^(a) 663-688 1627^(b) 5′-TTA CAT TGC GAC CAT GAA ATT GCT CT 1628^(a) 849-874 Resistance genes: vgb, vgh 1629 5′-AAG GGG AAA GTT TGG ATT ACA CAA CA 1633^(a) 73-98 1630^(b) 5′-GAA CCA CAG GGC ATT ATC AGA ACC 1633^(a) 445-468 1631 5′-CGA CGA TGC TTT ATG GTT TGT 1633^(a) 576-596 1632^(b) 5′-GTT AAT TTG CCT ATC TTG TCA CAC TC 1633^(a) 850-875 Resistance gene: vgbB 1634 5′-TTA ACT TGT CTA TTC CCG ATT CAG G 1882^(a) 23-47 1635^(b) 5′-GCT GTG GCA ATG GAT ATT CTG TA 1882^(a) 267-289 1636 5′-TTC CTA CCC CTG ATG CTA AAG TGA 1882^(a) 155-178 1637^(b) 5′-CAA AGT GCG TTA TCC GAA CCT AA 1882^(a) 442-464 Sequencing primers Resistance gene: gyrA 1290 5′-GAY TAY GCI ATG ISI GTI ATH GT 1299^(a) 70-83 1292^(b) 5′-ARI SCY TCI ARI ATR TGI GC 1299^(a) 1132-1152 1291 5′-GCI YTI CCI GAY GTI MGI GAY GG 1299^(a) 100-123 1292^(b) 5′-ARI SCY TCI ARI ATR TGI GC 1299^(a) 1132-1152 1293 5′-ATG GCT GAA TTA CCT CAA TC 1299^(a)  1-21 1294^(b) 5′-ATG ATT GTT GTA TAT CTT CTT CAA C 1299^(a) 2626-2651 1295^(b) 5′-CAG AAA GTT TGA AGC GTT GT 1299^(a) 1255-1275 1296 5′-AAC GAT TCG TGA GTC AGA TA 1299^(a) 1188-1208 1297 5′-CGG TCA ACA TTG AGG AAG AGC T 1300^(a) 29-51 1298^(b) 5′-ACG AAA TCG ACC GTC TCT TTT TC 1300^(a) 415-437 Resistance gene: gyrB 1301 5′-GTI MGI AWI MGI CCI GSI ATG TA 1307^(a)  82-105 1302^(b) 5′-TAI ADI GGI GGI KKI GCI ATR TA 1307^(a) 1600-1623 1303 5′-GGI GAI GAI DYI MGI GAR GG 1307^(a) 955-975 1304^(b) 5′-CIA RYT TIK YIT TIG TYT G 1307^(a) 1024-1043 1305 5′-ATG GTG ACT GCA TTG TCA GAT G 1307^(a)  1-23 1306^(b) 5′-GTC TAC GGT TTT CTA CAA CGT C 1307^(a) 1858-1888 Resistance gene: parC 1308 5′-ATG TAY GTI ATI ATG GAY MGI GC 1320^(a) 67-90 1309^(b) 5′-ATI ATY TTR TTI CCY TTI CCY TT 1320^(a) 1993-2016 1310 5′-ATI ATI TSI ATI ACY TCR TC 1320^(a) 1112-1132 1311^(b) 5′-GAR ATG AAR ATI MGI GGI GAR CA 1320^(a) 1288-1311 1312 5′-AAR TAY ATI ATI CAR GAR MGI GC 1321^(a) 67-90 1313^(b) 5′-AMI AYI CKR TGI GGI TTI TTY TT 1321^(a) 2212-2235 1314 5′-TAI GAI TTY ACI GAI SMI CAR GC 1321^(a) 1228-1251 1315^(b) 5′-ACI ATI GCI TCI GCY TGI KSY TC 1321^(a) 1240-1263 1316 5′-GTG AGT GAA ATA ATT CAA GAT T 1321^(a)  1-23 1317^(b) 5′-CAC CAA AAT CAT CTG TAT CTA C 1321^(a) 2356-2378 1318 5′-ACC TAY TCS ATG TAC GTR ATC ATG GA 1320^(a) 58-84 1319^(b) 5′-AGR TCG TCI ACC ATC GGY AGY TT 1320^(a) 832-855 Resistance gene: parE 1322 5′-RTI GAI AAY ISI GTI GAY GAR G 1328^(a) 133-155 1325^(b) 5′-RTT CAT YTC ICC IAR ICC YTT 1328^(a) 1732-1752 1323 5′-ACI AWR SAI GGI GGI ACI CAY G 1328^(a) 829-850 1324^(b) 5′-CCI CCI GCI SWR TCI CCY TC 1328^(a) 1280-1302 1326 5′-TGA TTC AAT ACA GGT TTT AGA G 1328^(a) 27-49 1327^(b) 5′-CTA GAT TTC CTC CTC ATC AAA T 1328^(a) 1971-1993 ^(a)Sequence from databases. ^(b)These sequences are from the complementary DNA strand of the sequence of the originating fragment given in the Sequence Listing.

Annex LI: Internal hybridization probes for specific detection of antimicrobial agents resistance genes sequences. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence NO. position Resistance gene: aph3′VIa 2252 5′-CCA CAT ACA GTG TCT CTC 1406^(a) 149-166 Resistance gene: blaSHV 1886 5′-GAC GCC CGC GCC ACC ACT 1900^(a) 484-501 1887 5′-GAC GCC CGC GAC ACC ACT A 1899^(a) 514-532 1888 5′-GAC GCC CGC AAC ACC ACT A 1901^(a) 514-532 1889 5′-GTT CGC AAC TGC AGC TGC TG 1899^(a) 593-612 1890 5′-TTC GCA ACG GCA GCT GCT G 1899^(a) 594-612 1891 5′-CCG GAG CTG CCG AIC GGG 1902^(a) 692-709 1892 5′-CGG AGC TGC CAA RCG GGG 1903^(a) 693-710 1893 5′-GGA GCT GGC GAR CGG GGT 1899^(a) 694-711 1894 5′-GAC CGG AGC TAG CGA RCG 1904^(a) 690-707 1895 5′-CGG AGC TAG CAA RCG GGG T 1905^(a) 693-711 1896 5′-GAA ACG GAA CTG AAT GAG GCG 1899^(a) 484-504 1897 5′-CAT TAC CAT GGG CGA TAA CAG 1899^(a) 366-386 1898 5′-CCA TTA CCA TGA GCG ATA ACAG 1899^(a) 365-386 Resistance gene: blaTEM 1909 5′-ATG ACT TGG TTA AGT ACT CAC C 1928^(a) 293-314 1910 5′-ATG ACT TGG TTG AGT ACT CAC C 1927^(a) 293-314 1911 5′-CCA TAA CCA TGG GTG ATA ACA C 1928^(a) 371-392 1912 5′-CCA TAA CCA TGA GTG ATA ACA C 1927^(a) 371-392 1913 5′-CGC CTT GAT CAT TGG GAA CC 1928^(a) 475-494 1914 5′-CGC CTT GAT CGT TGG GAA CC 1927^(a) 475-494 1915 5′-CGC CTT GAT AGT TGG GAA CC 1929^(a) 475-494 1916 5′-CGT GGG TCT TGC GGT ATC AT 1927^(a) 712-731 1917 5′-CGT GGG TCT GGC GGT ATC AT 1930^(a) 712-731 1918 5′-GTG GGT CTC ACG GTA TCA TTG 1927^(a) 713-733 1919 5′-CGT GGG TCT CTC GGT ATC ATT 1931^(a) 712-732 1920 5′-CGT GGI TCT CGC GGT ATC AT 1927^(a) 712-731 1921 5′-CGT GGG TCT AGC GGT ATC ATT 1932^(a) 713-733 1922 5′-GTT TTC CAA TGA TTA GCA CTT TTA 1927^(a) 188-211 1923 5′-GTT TTC CAA TGA TAA GCA CTT TTA 1927^(a) 188-211 1924 5′-GTT TTC CAA TGC TGA GCA CTT TT 1932^(a) 188-210 1925 5′-CGT TTT CCA ATG ATG AGC ACT TT 1927^(a) 187-209 1926 5′-GTT TTC CAA TGG TGA GCA CTT TT 1933^(a) 188-210 2006 5′-TGG AGC CGG TGA GCG TGG 1927^(a) 699-716 2007 5′-TGG AGC CAG TGA GCG TGG 2010^(a) 699-716 2008 5′-TCT GGA GCC GAT GAG CGT G 1929^(a) 697-715 2009 5′-CTG GAG CCA GTA AGC GTG G 2011^(a) 698-716 2141 5′-CAC CAG TCA CAG AAA AGC 1927^(a) 311-328 Resistance gene: dhfrIa 2253 5′-CAT TAC CCA ACC GAA AGT A 1461^(a) 158-176 Resistance gene: embB 2104 5′-CTG GGC ATG GCI CGA GTC 2105^(a) 910-927 Resistance gene: gyrA 1333 5′-TCA TGG TGA CTT ATC TAT TTA TG 1299^(a) 240-263 1334 5′-CAT CTA TTT ATA AAG CAA TGG TA 1299^(a) 251-274 1335 5′-CTA TTT ATG GAG CAA TGG T 1299^(a) 254-273 1940 5′-GTA TCG TTG GTG ACG TAA T 1299^(a) 206-224 1943 5′-GCT GGT GGA CGG CCA G 1954^(a) 279-294 1945 5′-CGG CGA CTA CGC GGT AT 1954^(a) 216-232 1946 5′-CGG CGA CTT CGC GGT AT 1954^(a) 216-232 1947 5′-CGG TAT ACG GCA CCA TCG T 1954^(a) 227-245 1948 5′-GCG GTA TAC AAC ACC ATC G 1954^(a) 226-244 1949 5′-CGG TAT ACG CCA CCA TCG T 1954^(a) 227-245 2042 5′-CAC GGG GAT TTC TCT ATT TA 2054^(a) 103-122 2043 5′-CAC GGG GAT TAC TCT ATT TA 2054^(a) 103-122 Resistance gene: inhA 2100 5′-GCG AGA CGA TAG GTT GTC 2101^(a) 1017-1034 Resistance gene: parC 1336 5′-TGG AGA CTA CTC AGT GT 1321^(a) 232-249 1337 5′-TGG AGA CTT CTC AGT GT 1321^(a) 232-249 1338 5′-GTG TAC GGA GCA ATG 1321^(a) 245-260 1339 5′-CCA GCG GAA ATG CGT 1321^(a) 342-357 1941 5′-GCA ATG GTC CGT TTA AGT 1321^(a) 253-270 1944 5′-TTT CGC CGC CAT GCG TTA C 1781 247-265 1950 5′-GGC GAC ATC GCC TGC 1781 137-151 1951 5′-GGC GAC AGA GCC TGC TA 1781 137-153 1952 5′-CCT GCT ATG GAG CGA TGG T 1781 147-165 1953 5′-CGC CTG CTA TAA AGC GAT GGT 1781 145-165 2046 5′-ACG GGG ATT TTT CTA TCT AT 2055^(a) 227-246 Resistance gene: rpoB 2067 5′-AGC TGA GCC AAT TCA TGG 2072^(a) 1304-1321 2068 5′-ATT CAT GGA CCA GAA CAA C 2072^(a) 1314-1332 2069 5′-CGC TGT CGG GGT TGA CCC 2072^(a) 1334-1351 2070 5′-GTT GAC CCA CAA GCG CCG 2072^(a) 1344-1361 2071 5′-CGA CTG TCG GCG CTG GGG 2072^(a) 1360-1377 Resistance gene: tetM 2254 5′-ACC TGA ACA GAG AGA AAT G 1590^(a) 1062-1080 ^(a)Sequence from databases.

Annex LII: Molecular beacon internal hybridization probes for specific detection of atpD sequences. Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence^(a) NO. position Bacterial species: Bacteroides fragilis 2136 5′-CCA ACG CGT CCT CAA TCA TTT CTA ACT TCT 929 353-382 ATG GCC GGC GTT GG Bacterial species: Bordetella pertussis 2182 5′-GCG CGC CAA CGA CTT CTA CCA CGA AAT GGA 1672 576-605 AGA GTC GCG CGC Bacterial group: Campylobacter jejuni and C. coli 2133 5′-CCA CGC ACA WAA ACT TGT TTT AGA AGT 1576,  44-73^(d) AGC AGC WCA GCG TGG 1600, 1849, 1863, 2139^(b,c) Fungal species: Candida glabrata 2078 5′-CCG AGC CTT GGT CTT CGG CCA AAT GAA CGC 463 442-463 TCG G Fungal species: Candida krusei 2075 5′-CCG AGC CAG GTT CTG AAG TCT CTG CAT TAT 468 720-748 TAG GTG CTC GG Fungal species: Candida lusitaniae 2080 5′-CCG AGC CGA AGA GGG CCA AGA TGT CGC TCG G 470 520-538 Fungal species: Candida parapsilosis 2079 5′-CCG AGC GTT CAG TTA CTT CAG TCC AAG CCG 472 837-860 GCT CGG Fungal species: Candida tropicalis 2077 5′-CCG AGC AAC CGA TCC AGC TCC AGC TAC GCT 475 877-897 CGG Bacterial species: Klebsiella pneumoniae 2281 5′-CCC CCA GCT GGG CGG CGG TAT CGA TGG GGG 317  40-59 ^(a)Underlined nucleotides indicate the molecular beacon's stem. ^(b)Sequence from databases. ^(c)These sequences were aligned to derive the corresponding primer. ^(d)The nucleotide positions refer to the C. jejuni atpD sequence fragment (SEQ ID NO. 1576). Originating DNA fragment SEQ ID Nucleotide SEQ ID NO. Nucleotide sequence^(a) NO. position Fungal genus: Candida sp. 2076 5′-CCG AGC YGA YAA CAT TTT CAG ATT CAC CCA 460-478, 697-723^(c) RGC GCT CGG 663^(b) ^(a)Underlined nucleotides indicate the molecular beacon's stem. ^(b)These sequences were aligned to derive the corresponding primer. ^(c)The nucleotide positions refer to the C. albicans atpD sequence fragment (SEQ ID NO. 460).

Annex LIII: Internal hybridization probes for specific detection of atpD sequences. Originating DNA fragment SEQ SEQ ID Nucleotide ID NO. Nucleotide sequence NO. position Bacterial species: Acinetobacter baumannii 2169 5′-CCC GTT TGC GAA AGG TGG 243 304-321 Bacterial species: Klebsiella pneumoniae 2167 5′-CAG CAG CTG GGC GGC GGT 317 36-53

Annex LIV: Internal hybridization probes for specific detection of ddl and mtl sequences. Originating DNA fragment Nucleo- SEQ SEQ ID tide ID NO. Nucleotide sequence NO. position Bacterial species: Enterococcus faecium (ddl) 2286 5′-AGT TGC TGT ATT AGG AAA TG 2288^(a) 784-803 2287 5′-TCG AAG TTG CTG TAT TAG GA 2288^(a) 780-799 Bacterial species: Enterococcus faecalis mtl) 2289 5′-CAC CGA AGA AGA TGA AAA AA 1243^(a) 264-283 2290 5′-TGG CAC CGA AGA AGA TGA 1243^(a) 261-278 2291 5′-ATT TTG GCA CCG AAG AAG A 1243^(a) 257-275 ^(a)Sequence from databases. 

1. A composition for the detection of a vancomycin resistant pathogen in a sample using a nucleic acid amplification assay, wherein said composition comprises a primer pair for the amplification of vanA sequences, said primer pair comprising a forward and a reverse oligonucleotides, wherein said forward and reverse oligonucleotides are between 13 and 30 nucleotides, and wherein said forward and reverse oligonucleotides each comprises a binding region that is complementary to primer binding sites present on opposite strands of the pathogen's DNA, wherein said primer pair is adapted to amplify a target region of a vancomycin resistance gene of said pathogen's DNA between and including said primer binding sites to produce a detectable vanA vancomycin amplification product, wherein at least one of said oligonucleotides comprises, or is fully complementary to, at least 11 consecutive nucleotides of SEQ ID NO: 1090 and SEQ ID NO: 1091, or the complements thereof.
 2. (canceled)
 3. (canceled)
 4. The composition of claim 1, further comprising at least one internal hybridization probe, wherein said internal hybridization probe can hybridize under stringent conditions to said vanA vancomycin amplification product.
 5. The composition of claim 4, wherein said internal hybridization probe is a molecular beacon.
 6. The composition of claim 4, wherein said internal hybridization probe comprises at least 10 consecutive nucleotides of SEQ ID NO:
 2299. 7. (canceled)
 8. The composition of claim 4, further comprising: an internal control DNA; and an internal control probe, wherein said internal control DNA is amplified using the said forward and reverse oligonucleotides to produce a control amplification product in said nucleic acid amplification assay, and wherein said internal control probe hybridizes to said internal control DNA under the same conditions as said internal hybridization probe hybridizes to said vancomycin amplification product.
 9. The composition of claim 8, wherein said internal control probe comprises at least 10 consecutive nucleotides of the sequence of SEQ ID NO:
 2301. 10. A kit comprising the composition of claim
 1. 11. A method to detect the presence of vancomycin-resistant organisms in a sample comprising nucleic acids, comprising: annealing the nucleic acids of said sample with the composition of claim 4; amplifying said sample nucleic acids with said annealed primer pair; and determining the amount of internal hybridization probe that is annealed to the vanA vancomycin amplification product and the target region.
 12. The method of claim 11, wherein said primer pair consists of SEQ ID NO's 1090 and 1091, or the complements thereof.
 13. The method of claim 11, wherein said primer pair and said internal hybridization probe are placed in the same physical enclosure.
 14. (canceled)
 15. The method of claim 11 wherein amplification step comprises a method selected from the group consisting of: (a) polymerase chain reaction (PCR), (b) ligase chain reaction, (c) nucleic acid sequence-based amplification, (d) self-sustained sequence replication, (e) strand displacement amplification, (f) branched DNA signal amplification, (g) nested PCR, and (h) multiplex PCR.
 16. The method of claim 15, wherein said amplification step comprises PCR.
 17. (canceled)
 18. The method of claim 11, wherein said internal hybridization probe comprises at least 10 consecutive nucleotides of the sequence of SEQ ID NO:
 2299. 19. The composition of claim 1, wherein said forward or said reverse oligonucleotide consists of SEQ ID NO:
 1090. 20. The composition of claim 1, wherein said forward or said reverse oligonucleotide consists of SEQ ID NO:
 1091. 21. The composition of claim 1, wherein said forward and reverse oligonucleotides consist of SEQ ID NO: 1090 and SEQ ID NO: 1091, respectively.
 22. The composition of claim 21, further comprising an internal hybridization probe, wherein said internal hybridization probe can hybridize under stringent conditions to said vancomycin amplification product.
 23. The composition of claim 22, wherein said internal hybridization probe is a molecular beacon.
 24. The composition of claim 22, wherein said internal hybridization probe comprises at least 10 consecutive nucleotides of the sequence of SEQ ID NO:
 2299. 25. The composition of claim 22, further comprising: an internal control DNA; and an internal control probe, wherein said internal control DNA is amplified under the same conditions and using said forward and reverse primers to produce a control amplification product, and wherein said internal control probe hybridizes to said internal control DNA under the same conditions as said internal hybridization probe hybridizes to said vanA vancomycin amplification product.
 26. The composition of claim 25, wherein said internal control DNA is SEQ ID NO:
 2302. 27. The composition of claim 25, wherein said internal control probe comprises at least 10 consecutive nucleotides of the sequence of SEQ ID NO:
 2301. 28. The composition of claim 8, wherein said internal control DNA is SEQ ID NO:
 2302. 29. The composition of claim 1, further comprising a second amplification primer pair for the amplification of vanB sequences, said second primer pair comprising a second forward and a second reverse oligonucleotide, wherein said second forward and second reverse oligonucleotides are each between 13 and 30 nucleotides and wherein each of said forward and reverse oligonucleotides comprises a binding region that is complementary to primer binding sites present on opposite strands of the pathogen's DNA, wherein said primer pair is adapted to amplify a vancomycin resistance gene of said pathogen's DNA between and including said primer binding sites to produce a detectable vanB vancomycin amplification product, wherein at least one of said oligonucleotides of said second primer pair is selected from the group consisting of: SEQ ID NO: 1095 and SEQ ID NO: 1096, or the complements thereof.
 30. The composition of claim 29, wherein said second forward and second reverse oligonucleotides of said second primer pair consist of SEQ ID NO: 1095 and SEQ ID NO: 1096, respectively.
 31. The composition of claim 29 further comprising an internal hybridization probe, wherein said internal hybridization probe can hybridize under stringent conditions to said vanA vancomycin amplification product or said vanB vancomycin amplification product.
 32. The composition of claim 31, wherein said internal hybridization probe is a molecular beacon.
 33. The composition of claim 31, wherein said internal hybridization probe comprises at least 10 consecutive nucleotides of the sequence of SEQ ID NO:
 2299. 34. The composition of claim 31, wherein said internal hybridization probe comprises at least 10 consecutive nucleotides of the sequence of SEQ ID NO:
 2300. 35. The composition of claim 29, further comprising: an internal control DNA; and an internal control probe, wherein said internal control DNA is amplified under the same conditions and using the same forward and reverse oligonucleotides to produce a control amplification product, and wherein said internal control probe hybridizes to said internal control DNA under the same conditions as said internal hybridization probe hybridizes to said vanA or vanB vancomycin amplification product.
 36. The composition of claim 36, wherein said internal control DNA comprises SEQ ID NO:
 2302. 37. The composition of claim 36, wherein said internal control probe comprises at least 10 consecutive nucleotides of the sequence of SEQ ID NO:
 2301. 38. The method of claim 11, further comprising annealing the sample nucleic acids with: an internal control DNA; and an internal control probe, wherein said internal control DNA is amplified under the same conditions and using the same forward and reverse oligonucleotides as to produce a control amplification product, and wherein said internal control probe hybridizes to said internal control DNA under the same conditions as said internal hybridization probe hybridizes to said vanA vancomycin amplification product.
 39. The method of claim 38, wherein said internal control probe comprises at least 10 consecutive nucleotides of the sequence of SEQ ID NO:
 2301. 40. The method of claim 38, wherein said internal control DNA comprises of SEQ ID NO:
 2302. 